Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification

Garcinia gummi-gutta (L.) Roxb. (Clusiaceae) is an endemic, semidomesticated, fruit-yielding tree species distributed in the Western Ghats of India and Sri Lanka. Various bioactive phytochemicals, such as garcinol, benzophenones and xanthones are isolated from G. gummi-gutta and have shown antibacterial, antiviral and antioxidant activities. We sequenced the total genomic DNA using Illumina Hiseq 2000 platform and examined 241,141,804 bp high quality data, assembled into 773,889 contigs. In these contigs, 27,313 simple-sequence repeats (SSRs) were identified, among which mononucleotide repeats were predominant (44.98%) followed by dinucleotide and trinucleotide repeats. Primers were designed for 9964 microsatellites among which 32 randomly selected SSR primer pairs were standardized for amplification. Polymerase chain reaction (PCR) amplification of genomic DNA in 30 G. gummi-gutta genotypes revealed polymorphic information content (PIC) across all 32 loci ranging from 0.867 to 0.951, with a mean value of 0.917. The observed and expected heterozygosity ranged from 0.00 to 0.63 and 0.896 to 0.974, respectively. Alleles per locus ranged from 12 to 27. This is the first report on the development of genomic SSR markers in G. gummi-gutta using next-generation sequencing technology. The genomic SSR markers developed in this study will be useful in identification, mapping, diversity and breeding studies

Molecular and morphological diversity in locally grown non-commercial (heirloom) mango varieties of North India

Mango (Mangifera indica L.) has been cultivated and conserved in different agro-ecologies including Malihabad region in northern part of India, that is well known for housing diverse types (heirloom and commercial varieties). In the present study, 37 mango types comprising of 27 heirloom varieties from Malihabad region and 10 commercial varieties grown in North and Eastern India were assessed for morphological attributes and molecular diversity. The employed SSR markers amplified 2-13 alleles individually, cumulatively amplifying 124 alleles. These were studied for allelic diversity and genetic dissimilarity ranged from 0.035 to 0.892 arranging the varieties in three major clusters. The results revealed that majority of unique heirloom mangoes from Malihabad were different from the eastern part of the country. It is interesting to note Dashehari, a commercial variety from Malihabad was not aligned with heirloom varieties. Commercial varieties like Gulabkhas and Langra were placed in a separate group including Bombay Green, Himsagar, Dashehari, etc., indicating their dissimilarity with heirloom varieties at molecular level and thus, indicating importance for later from conservation point of view. Furthermore, the hierarchical clustering of varieties based on fruit morphology, assembled these into four groups largely influenced by fruit size. The maximum agreement subtree indicated seemingly good fit as thirteen varieties were arrayed in common grouping pattern. Appreciable dissimilarity among the heirloom varieties demonstrated by molecular analysis, underlines the importance for their on-farm conservation

Analysis of genetic diversity among Indian niger [ Guizotia abyssinica (L. f.) Cass.] cultivars based on randomly amplified polymorphic DNA markers

Randomly amplified polymorphic DNA (RAPD) markers were used to estimate genetic diversity among 18 cultivars of niger from India. Total genomic DNA was extracted and subjected to RAPD analysis using 80 arbitrary 10-mer primers; 17 primers were selected, which yielded a total of 124 bands, 41.20% of them polymorphic. None of the primers produced unique banding pattern for each cultivar. RAPD data were used to calculate a Squared-Euclidean Distance matrix which revealed a minimum genetic distance between cultivars JNC-6 and N-48 and a maximum distance between IGP-76 and JN-30. Based on the distance matrix, a cluster analysis was done using a minimum variance algorithm. The dendrogram generated, based on Ward\u2019s method, grouped 18 niger cultivars into two major clusters. The first cluster consisted of early maturing cultivars (e.g. N-129 and N-134; 80-90 days), and the second of late maturing cultivars (e.g. GA-8 and GA-9; 135-145 days). The present study shows that there is high diversity among the niger cultivars tested and indicates the potential of RAPD markers for identification and maintenance of niger germplasm for crop improvement purposes

Not Available

Not AvailableProtocol for extracting intact genomic DNA of reasonable quality and purity from minor and underexploited and secondary metabolite rich crops like pomegranate is not available. The presence of large amount of interfering components like polyphenols, polysaccharides, and other secondary metabolites make DNA isolation from pomegranate challenging. The method described involves a modification of the available CTAB method employing silica matrix which yielded high quality DNA. The protocol has been successfully tested with a wild pomegranate genotype and Hind III enzyme digestion. Results show that the DNA isolated is good enough for downstream analysis.Not Availabl

Not Available

Not AvailableAbstract: DNA based RAPD (Randomly Amplification of Polymorphic DNA) markers have been used extensively to study genetic relationships in number of crop plants. In this study, 44 okra genotypes collected from different parts of India, were selected to assess genetic distinctiveness and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 14 arbitrary 10 mer primers. The molecular analysis showed that all the fourteen primers used revealed clear distinction between the genotypes and they generated a total of 104 RAPD bands most of which were polymorphic across accessions (74.03%). The number of bands resolved per amplification was primer dependent and varied from 4 (OPV-07, OPV-08) to 11 (OPD-05) with average number of bands per primer was 7.41. RAPD data were used to calculate a Squared Euclidean Distance matrix, and based on this, cluster analysis was done using minimum variance algorithm. Cluster analysis showed two major groups. Each sub-group was characterized using morphological and genetic characteristics of the respective genotypes.Not Availabl

Not Available

Not AvailablePlant microRNAs (miRNAs) are short, non-coding, conserved RNAs that play an important role in the transcriptional and post-transcriptional regulation of gene expression. Five miRNAs were identified in pomegranate (Punica granatum L.) using a bioinformatics approach on 7,361 contigs from partial genome sequence data (19 Mbp) generated using Roche 454 GS FLX Titanium pyrosequencing technology. Thirty-five potential mRNA targets were identified by homology searches of all five identified pomegranate miRNAs against the Arabidopsis thaliana mRNA dataset using psRNAtarget software (http://plantgrn.noble.org/psRNATarget/). The miRNA targets identified were then subjected to Gene Ontology analysis. We found that most mRNA targets were constitutively expressed genes involved in different molecular functions, biological processes, and cellular components. Experimental validation of these computationally-identified miRNAs has the potential to elucidate miRNA-based gene regulation and evolution in a non-model crop such as pomegranate.Not Availabl

Not Available

Not AvailablePreliminary shelf life tests were performed to select the best gas composition and the best sodium acetate concentrations in the modified atmosphere. Bacterial quality assessment was carried out by the monitoring of total aerobic bacteria, H2S producing bacteria, lactic acid bacteria, pseudomonads, Enterobacteriaceae, Staphylococcus aureus, streptococci, sulphite reducing clostridia and botulinum toxin by mouse bioassay. Bacteria grew most quickly in seer fish stored in air, followed by those in MAP and the lowest counts were with MAP pre-treated with sodium acetate. The application of sodium acetate treatment to seer fish steaks resulted in a bacteriostatic effect, contributing to the improvement of the microbiological quality of seer fish steaks. There was less trimethylamine in the modified atmosphere packed samples pretreated with sodium acetate than in air packed samples by the factor of seven, at the end of the shelf life. Modified atmosphere packaging alone increased the shelf life from 8 (air pack) to 22 days; however, addition of sodium acetate further extended the shelf life to 28 days. The results showed that the combined effect of MAP (70 vol.% CO2:30 vol.% O2) and sodium acetate (1%, w/v) is a valuable tool to allow an effective extension of the shelf life of raw fish products.Not Availabl

Not Available

Not AvailableA survey conducted during 2013-14 to collect and characterize the Kuttiattoor mango accessions from Kerala, revealed large unique variability in morphological, biochemical and DNA barcode data. All the accessions were polyembryonic with fruit maturity during February-March. The mature fruit length (cm), width (cm) and leaf length (cm) ranged from 5.10 – 9.60 (cm), 4.60 – 8.40 (cm) and 12.47- 30.40 (cm) respectivelyNot Availabl