Rapid plant regeneration from Gerbera jamesonii Bolus callus cultures

A high frequency shoot organogenesis and plant establishment protocol has been developed for Gerbera jamesonii from ex vitro leaf derived callus. The optimal callus was developed on Murashige and Skoog (MS) basal medium supplemented with 0.4 mg L–1 6-benzylaminopurine (BAP), 4.0 mg L–1 -naphthalene acetic acid (NAA) and 3% (w/v) sucrose. Two callus types differing in their structures and growth rates were observed. A friable and non-chlorophyllous callus with high growth rate appeared at the cut surfaces of the explant, and a compact chlorophyllous callus. The rate of shoot bud regeneration was positively correlated with the concentration of growth regulators in the nutrient media. The explants were highly responsive (83.3%) in a medium containing 2 mg L–1 NAAand 1 mg L–1 BAP after 3 weeks of callus transfer to a medium. Regenerated plantlets were transferred to soil where they grew normally with a survival rate of 95%. This protocol offers rapid build up of selected clones and opens up prospects for using biotechnological approaches for gerbera improvement

in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)

Microsatellites are an important class of molecular markers having wide application in genetic research. Development of microsatellites using conventional methods is laborious and expensive. Alternatively, in silicoapproach can be followed to detect simple sequence repeats (SSRs) from expressed sequence tags (ESTs) available in public biological databases. The in silico developed EST-SSRs have been found to be transferrable across species and genera. A study was undertaken to mine simple sequence repeats (SSRs) from the expressed sequence tags (ESTs) of arum lily, Zantedeschia aethiopica, belongs to the family Araceae. A total of 4283 ESTs of Zantedeschia aethiopica, downloaded from dbEST of NCBI, were pre-processed and subjected to clustering and assembly. In all, 1968 clusters (800 contigs and 1168 singletons) were obtained, resulting in 54 % reduction in ESTs. In addition, 1936 SSRs were obtained, which included 617 mono, 101 di-, 201 tri-, 80 tetra-, 23 penta- and 898 hexa-nucleotide repeats. The plant has an abundance of 0.70 SSRs/ kb. We designed 1091 primers for these SSRs. A few in silico designed SSR primers were tested for polymorphism in Anthurium, belonging to the Araceae family, resulting in 40% amplification success

Genetic Diversity Analysis and Barcoding in Tuberose (Polianthes tuberosa L.) Cultivars Using RAPD and ISSR Markers

Tuberose is one of the most important bulbous ornamentals grown commercially for loose as well as cut flowers. RAPD and ISSR markers used in the study revealed 53% and 73% polymorphism, respectively, among ten tuberose varieties. Polymorphic Information Content (PIC) and Resolving Power (RP) for RAPD varied from 0.35 - 0.46 and 0.8 - 3.6, respectively, and that for ISSR was 0.36 - 0.49 and 0.91 - 4.55, respectively. The dendrogram (UPGMA), based on Jaccards co-efficient as similarity index for RAPD and ISSR, grouped ten varieties into two major clusters, and, combined RAPD-ISSR cluster analysis formed three major clusters based on their genetic relatedness/variation. PCA revealed that the spatial arrangement of these 10 cultivars was congruent with dendrogram analysis. Mantel's test indicated very good correlation, with r = 0.86 for combination of ISSR and RAPD-ISSR. To facilitate identification of tuberose cultivars, a cultivar identification diagram (CID) was developed in which seven ISSR loci could differentiate all the ten cultivars used in the study. Barcodes were developed for five cultivars released by IIHR using 57 polymorphic loci generated by 11 ISSR primers. The size of these loci ranged from 252bp to 2.2kb. These barcodes can be used as a standard reference source for quick identification of cultivars

Assessment of Genetic Diversity in Guava (Psidium guajava) Germplasm Using Microsatellites

Although the varietal diversity is fairly rich in guava, most varieties lack one or more desirable characters. Hence, attempts were made for improving specific traits, viz., attractive pink pulp colour, soft seeds, medium fruit size, high TSS and high ascorbic acid. Genetic diversity analysis is a prerequisite for identifying potential parents in breeding programs and germplasm conservation. Molecular characterization helps discriminate closely-related genotypes, as, this technique is unaffected by environment, rendering it more reliable. In this study, 48 polymorphic SSRs screened from a total of 115 SSR markers were used for analyzing marker segregation in 72 guava accessions. Statistical analysis was done using IDENTITY1.0 and CERVUS 3.0 software. Cluster analysis was done with DARwin 5.0 software, using Wards Minimum Variance method, and weighted group neighbour joining method, to check reliability of grouping among clusters. The trend in grouping was found to be similar in both methods. Dendrograms generated showed that the hybrids clustered with their parents; exotic collections fell into two different sub-groups based on productivity; the wild species formed one group; and Navalar cultivars from Dharwad clustered together, reflecting similar origin

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Not AvailableMicrosatellites are an important class of molecular markers having wide application in genetic research. Development of microsatellites using conventional methods is laborious and expensive. Alternatively, in silicoapproach can be followed to detect simple sequence repeats (SSRs) from expressed sequence tags (ESTs) available in public biological databases. The in silico developed EST-SSRs have been found to be transferrable across species and genera. A study was undertaken to mine simple sequence repeats (SSRs) from the expressed sequence tags (ESTs) of arum lily, Zantedeschia aethiopica, belongs to the family Araceae. A total of 4283 ESTs of Zantedeschia aethiopica, downloaded from dbEST of NCBI, were pre-processed and subjected to clustering and assembly. In all, 1968 clusters (800 contigs and 1168 singletons) were obtained, resulting in 54 % reduction in ESTs. In addition, 1936 SSRs were obtained, which included 617 mono, 101 di-, 201 tri-, 80 tetra-, 23 penta- and 898 hexa-nucleotide repeats. The plant has an abundance of 0.70 SSRs/ kb. We designed 1091 primers for these SSRs. A few in silico designed SSR primers were tested for polymorphism in Anthurium, belonging to the Araceae family, resulting in 40% amplification success.Not Availabl

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Not AvailableSingle nucleotide polymorphisms (SNPs) are abundant in plant genomes and are thus used frequently in genetic analysis and crop breeding programs. Potential SNPs from expressed sequence tags (ESTs) of Allium cepa were mined for a total of 232 potential SNPs identified from 20,157 ESTs from NCBI. The SNPs occurred on an average frequency of 1 per 57 bp in the EST sequences. The ratio of transitions to transversions was 1.7: 1, and 65 of the 232 SNP sites were cut by different restriction enzymes. Primers could be designed for 227 SNPs and used for onion breeding programs after validation in wet lab.Not Availabl

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Not AvailableMicrosatellites or simple sequence repeats (SSRs) play an important role in plant genetics and breeding. The development of microsatellites is a time-consuming and expensive process. In silico mining of microsatellites from expressed sequence tags (ESTs), which are available in electronic molecular databases, is a cheaper alternative. In the present study, we used a computational approach for mining SSRs from 20,159 ESTs in Allium cepa. These onion ESTs represented a total length of 13.2 Mb and were downloaded from the dbEST database of the National Center for Biotechnology Information (NCBI) and subjected to various pre-processing steps. The pre-processed ESTs were clustered, resulting in non-redundant unigenes. These unigenes were analysed for their SSR content and distribution. In all, 1,464 SSRs consisting of di-, tri-, tetra-, penta- and hexa-nucleotide repeats were mined from the non-redundant ESTs (contigs and singletons). Tri-nucleotide SSRs were the most abundant, followed by tetra-, di-, hexa- and penta-nucleotide SSRs. Among the tri-coding repeats, leucine and serine codons were more abundant. The SSR-containing sequences were annotated and grouped into their respective functional categories. The predominant functional group among the annotated unigenes was “metabolism”, followed by “transcription factors” and “transporter proteins”. Primer pairs could be designed for 1,092 SSR-containing sequences. Of these, 51 primer pairs were validated in the laboratory. A database has been developed to store the unigenes, primer pairs, putative annotations, and BLAST results. After validation, the EST-derived microsatellite (SSR) markers can be used in studies related to marker-assisted selection, detection of polymorphism, DNA fingerprinting, and diversity analysis in onion.Not Availabl

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Not AvailablePlant micro-RNAs (miRNAs) are conserved and play important roles in abiotic stress responses or in plant responses to pathogen attack. Six miRNAs were identified in Solanum melongena (brinjal, eggplant) using bioinformatic methods from 98,089 EST sequences. Sixty-one potential mRNA targets were identified by homology searches of all six identified miRNAs against the Arabidopsis mRNA dataset using on-line miRU software (http://www.mirbase.org). The newly-identified miRNAs were studied further to compare their level of conservation with respect other family members. Later, the core promoter found in all targeted genes was identified and a highly-conserved GNAA motif with a critical role in the biogenesis of miRNAs was identified. The findings from this study will be useful for further research on the features of miRNAs and their mechanisms of gene regulation in S. melongena.Not Availabl

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Not AvailablePapaya (Carica papaya L.) is the most economically important fruit crop of the family Caricaceae, growing in the tropical and sub-tropical regions of the world. Originating from Central and South America, it bears highly nutritious fruits which are rich source of vitamins (A, folate, pantothenic acid and C) and minerals, low in sodium, fat and calories and contains no starch. The annual worldwide production of papaya amounts to 6.9 million tonnes, of which 36.1% is produced in India (NHB 2009). Despite this high production, most of the Indian production is based on few varieties resulting in restricted genetic variability. The cultivated papayas belong to genus Carica in family CaricaceaeNot Availabl