ArticleBioinformation2009
Identification of single nucleotide polymorphism in ginger using expressed sequence tags.
Article in Bioinformation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 24 citations in OpenAlex.
- A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges.Current research in food science · 2023Review
- Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits.BMC plant biology · 2018Article
- In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.Scientific reports · 2016Article
- Molecular markers: a potential resource for ginger genetic diversity studies.Molecular biology reports · 2016Review
- High quality SNPs/Indels mining and characterization in ginger from ESTs data base.Bioinformation · 2015Article
- Genomic profile of the plants with pharmaceutical value.3 Biotech · 2014Review
- Analyses of hypomethylated oil palm gene space.PloS one · 2014Article
- Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus.Journal of genetics · 2011Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledGinger (Zingiber officinale Rosc) (Family: Zingiberaceae) is a herbaceous perennial, the rhizomes of which are used as a spice. Ginger is a plant which is well known for its medicinal applications. Recently EST-derived SNPs are a free by-product of the currently expanding EST (Expressed Sequence Tag) databases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion/deletion) has led to a revolution in their use as molecular markers. Available (38139) Ginger EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script AutoSNP version 1.0 which has used 31905 ESTs for detecting SNPs and Indel sites. We found 64026 SNP sites and 7034 indel polymorphisms with frequency of 0.84 SNPs / 100 bp. Among the three tissues from which the EST libraries had been generated, Rhizomes had high frequency of 1.08 SNPs/indels per 100 bp whereas the leaves had lowest frequency of 0.63 per 100 bp and root is showing relative frequency 0.82/100bp. Transitions and transversion ratio is 0.90. In overall detected SNP, transversion is high when compare to transition. These detected SNPs can be used as markers for genetic studies. AVAILABILITY: The results of the present study hosted in our webserver www.spices.res.in/spicesnip.
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