Molecular characterization of ginger genotypes using RAPD and SSR markers

Genetic diversity among ginger genotypes collected from different parts of the country was studied using molecular markers (30 RAPD and 55 SSR). Compared to RAPD primers SSR primers were efficient in distinguishing the genotypes. A total of 86 and 23 polymorphic bands were observed with RAPD and SSR primers, respectively. Percentage polymorphism observed between RAPD and SSR primers was 97.40 % and 56.54 %. Grouping of genotypes by using combined data of RAPD and SSR primers indicated that irrespective of their place of collection or geographical origin, 30 genotypes were clustered into different groups which showed that, each individual genotype is having wider variability or it might be due to the genetic similarity existing among them

Diversity and phylogeography of begomovirus-associated beta satellites of okra in India

<p>Abstract</p> <p>Background</p> <p>Okra (<it>Abelmoschus esculentus</it>; family <it>Malvaceae</it>) is grown in temperate as well as subtropical regions of the world, both for human consumption as a vegetable and for industrial uses. Okra yields are affected by the diseases caused by phyopathogenic viruses. India is the largest producer of okra and in this region a major biotic constraint to production are viruses of the genus <it>Begomovirus</it>. Begomoviruses affecting okra across the Old World are associated with specific, symptom modulating satellites (beta satellites). We describe a comprehensive analysis of the diversity of beta satellites associated with okra in India.</p> <p>Results</p> <p>The full-length sequences of 36 beta satellites, isolated from okra exhibiting typical begomovirus symptoms (leaf curl and yellow vein), were determined. The sequences segregated in to four groups. Two groups correspond to the beta satellites Okra leaf curl beta satellite (OLCuB) and Bhendi yellow vein beta satellite (BYVB) that have previously been identified in okra from the sub-continent. One sequence was distinct from all other, previously isolated beta satellites and represents a new species for which we propose the name Bhendi yellow vein India beta satellite (BYVIB). This new beta satellite was nevertheless closely related to BYVB and OLCuB. Most surprising was the identification of Croton yellow vein mosaic beta satellite (CroYVMB) in okra; a beta satellite not previously identified in a malvaceous plant species. The okra beta satellites were shown to have distinct geographic host ranges with BYVB occurring across India whereas OLCuB was only identified in northwestern India. Okra infections with CroYVMB were only identified across the northern and eastern central regions of India. A more detailed analysis of the sequences showed that OLCuB, BYVB and BYVIB share highest identity with respect βC1 gene. βC1 is the only gene encoded by beta satellites, the product of which is the major pathogenicity determinant of begomovirus-beta satellite complexes and is involved in overcoming host defenses based on RNAi.</p> <p>Conclusion</p> <p>The diversity of beta satellites in okra across the sub-continent is higher than previously realized and is higher than for any other malvaceous plant species so far analyzed. The beta satellites identified in okra show geographic segregation, which has implications for the development and introduction of resistant okra varieties. However, the finding that the βC1 gene of the major okra beta satellites (OLCuB, BYVB and BYVIB) share high sequence identity and provides a possible avenue to achieve a broad spectrum resistance.</p

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12–&lt;20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, “Cashew Microsatellite Database (CMDB),” was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species

Molecular characterization and phylogenetic analysis of betasatellite molecules associated with okra yellow vein mosaic disease in Sri Lanka

Okra production in Sri Lanka has been severely affected by okra yellow vein mosaic disease (OYVMD), which is caused by begomoviruses and associated betasatellites. These betasatellite molecules commonly determine the development and severity of the disease. Therefore, knowledge about the genetic variability of betasatellites associated with OYVMD could assist okra breeding programs in the selection of resistant varieties. The present study aimed to characterize the betasatellite DNA sequences associated with OYVMD in Sri Lanka and to determine their phylogenetic relationships. Betasatellite DNA of six virus isolates from widely separated geographical locations were sequenced and compared with already reported begomovirus betasatellites. The betasatellite molecules have features common to other betasatellite DNAs: a conserved nonanucleotide TAATATTAC, a coding sequence for the protein βC1, an adenine rich region and a satellite conserved region. Nucleotide diversity among the isolates was relatively low (π = 0.034). A recombination event was detected at a specific region in the genome of all isolates. The isolates shared >96% sequence identity with bhendi yellow vein betasatellites reported from India and phylogenetic analysis confirmed their genetic relationship

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Not AvailableCoorg mandarin is a famous ecotype of mandarin grown in multi-tier cropping system in coffee and pepper plantations in Coorg region of India. The roving survey indicated disease incidence of huanglongbing (HLB) and Phytophthora ranging from 35%-64.2% and 22.5%-35.6% in different places of Coorg region. A total of 177 Phytophthora infected (plant roots 59, soil 118), and 576 greening or HLB infected Coorg mandarin samples were collected from 184 Coorg mandarin orchards, of these 111 Phytophthora isolates were isolated and characterized in this study on the basis of colony growth patterns and morphological structures. Based on the virulence, only 52 of 111 Phytophthora isolates were amplified by PCR using universal internal transcriber spacer (ITS) primers, cloned and sequenced. The sequences analysis of Phytophthora isolates revealed more than 97% nucleotide (nt) similarity within themselves, except eight isolates of P. palmivora and four isolates of P. nicotianae had varied nt identity (70.6% to 97.4%) with other Phytophthora species compared. Similarly, 523 of 576 Coorg mandarin samples were confirmed the presence of HLB infection by PCR using 16S rRNA gene specific universal primers. The representative five of 523 Coorg mandarin isolates showed nt identity ranged from 94.4% to 95.3% with Candidatus Liberibacter asiaticus (AB008366) isolate infecting citrus in Asia and one isolate of HLB shared nt identity of 96.9% with Ca. L. asiaticus (KJ944269).Not Availabl

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Not AvailableAn in vitro bioassay was undertaken to record the compatibility of local isolate of Trichoderma harzianum with fungicides used in coorg mandarin-pepper-coffee plantations. Eight non-systemic, 10 systemic and 9 combi products fungicides were evaluated against Trichoderma for radial growth inhibition on PDA medium using poisoned food technique. Contact fungicides at selected concentration were found to be safer than systemic and combi products except Chlorothalonil. In systemic fungicidal treatments complete mycelial inhibition of T. harzianum was recorded in Carbendazim, Hexaconazole, Thiophenate Methyl and Propiconazole. In combi products T. harzianum was not compatible with Hexaconazole 4%+Zineb 68%, Carbendazim 12 % + Mancozeb 63 %, Tebuconazole 50 % + Trifloxystrobin 25 % WG, Pyraclostrobin 133g/l + Epoxiconazole 50 g/ l and Captan 70 % + Hexaconazole 5% WP in any level of selected concentrations. Whereas, reduction in sporulation of T. harzianum was recorded in Metalaxyl 4%- Mancozeb 64% WP and Fenamidone 10 % + Mancozeb 50 WG with increase in concentrations.Not Availabl

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Not AvailableThe genus Colletotrichum contains an extremely diverse number of fungi including both plant pathogens and saprophytes. Plant pathogenic species are important worldwide, causing diseases commonly known as anthracnose of vegetables, fruits, and perennial tree crops. Anthracnose diseases appear in developing fruit in the field (pre-harvest) and those damaging mature fruit during storage (post-harvest). The anthracnose disease infected samples of Malayan apple fruit and leaves were collected from Central Horticultural Experiment Station, Chettalli, Karnataka state of India. The fungus was isolated from infected leaves and fruits by standard fungal isolation method. The Koch’s postulates of the fungus were confirmed by re-inoculated on the fruit and leaves of the same host. Further the fungus was identified based on pathogenic, morphological and amplification of internal transcribed spacer (ITS) region by PCR using universal ITS specific primers. The amplified PCR product were cloned and sequenced. The sequence analysis showed that Malayan apple isolate was showed maximum nucleotide identity of 100% with Collectotrichum acutatum infecting Lupines albus flowering plant.Not Availabl

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Not AvailableYellow vein mosaic disease (YVMD), which is caused by association of many distinctive mono and bipartite begomoviruses and their satellites is the most devastating disease of okra [Abelmoschus esculentus (L.) Moench] affecting both pod yield and quality. Since it is very difficult to control the disease properly by chemical means, the only practical remedy of this problem is to develop tolerant/resistant varieties. A lot of work has been done to determine the inheritance of resistance to YVMV in okra and to identify different sources of resistance. For better utilization and improvement of current okra genetic resources, there is a need to understand and appreciate the studies related to resistance source in wild and cultivated species, associated viruses, virus-vector relationship, hot-spots for virus, favourable conditions for disease development, screening methods and breeding strategies. In this review, efforts were made to elucidate the genetics of resistance to YVMV in okra and also to provide complete information regarding sources of resistance.Not Availabl

Molecular characterization of ageratum enation virus and beta satellite associated with leaf curl disease of fenugreek in India

Cisplatn is one of the chemotherapy for the treatment of triple‐negatve breast cancer (TNBC), but its effectveness is limited because of the phenomenon of chemoresistance. miR‐638 was shown to regulate chemoresistance; however, it has never been validated in the cisplatn‐resistant tumor from patents. This present study aimed to identfy the key gene regulatory networks of miR‐638 and evaluate the potental role of the miR‐638 and its targets as potental prognosis biomarkers for cisplatn‐resistance triple‐negatve breast cancer patents. The miR‐638 target was obtained from the miRecords database while the mRNA of chemoresistance biomarker candidate was obtained from the GSE18864 of GEO database, which is mRNA of cisplatn‐resistance TNBC patents. CCND1 and FZD7 are potental candidates for cisplatn chemoresistance biomarkers in patents with TNBC. Moreover, a Kaplan‐Meier survival plot showed that breast cancer patents with low mRNA levels of FZD7 had signifcantly worse overall survival than those in higher mRNA expression group. Taken together, miR‐638 plays a role in cisplatn resistance mechanism through a mechanism involving its target gene CCND1 and FZD7. Overall, miR‐638, CCND1, and FZD7 are candidates for cisplatn biomarker resistance in TNBC

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Not AvailableFilamentous fungi of the genus Colletotrichum and its teleomorph Glomerella are considered major plant pathogens worldwide. The fungi cause disease symptoms that are generally known as anthracnose in a wide range of vegetables, fruits and other crops. The fruit anthracnose of different crops was relatively well studied in India but the information about anthracnose on Carambola is still very scarce and it causes extensive yield losses at both the pre- and post-harvest stages during warm and rainy seasons. The anthracnose infected samples of Carambola was collected from Central Horticultural Experiment Station, Chettalli, Karnataka state of India. The fungus was isolated from the lesions of infected leaves and fruits. The pathogenicity of fungus was confirmed by re-inoculating on the same host. Further the fungus was identified based on pathogenic, morphological and amplification of internal transcribed spacer (ITS) region by PCR using ITS specific primers. The amplified PCR product were cloned and sequenced. The sequence analysis of Carambola isolate showed maximum nucleotide identity of 100% with Colletotrichum gloeosporioides (Penz.) Penz. & Sacc infecting tobacco crop.Not Availabl