Identification of single nucleotide polymorphism in ginger using expressed sequence tags.

Arumugam Chandrasekar,Santhosh J Eapen,Sahadevan Anoop,Kandiyl Sithara,Aikkal Riju

doi:10.6026/97320630004119

Arumugam Chandrasekar, Santhosh J Eapen + Show 3 more

Open Access

https://doi.org/10.6026/97320630004119

Copy DOI

Journal: Bioinformation	Publication Date: Sep 30, 2009
Citations: 19	License type: cc-by

Affiliation: Indian Institute of Spices Research

Abstract

Ginger (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. The results of the present study hosted in our webserver www.spices.res.in/spicesnip.

Highlights

Ginger (Zingiber officinale) is a perennial plant in the family Zingiberaceae - its rhizome is commonly used as a cooking spice throughout the world
In this study it is discovered that total of 64026 Single nucleotide polymorphisms (SNPs) sites and 7034 indel polymorphisms in 38139 Expressed sequence tags (ESTs) analyzed with an average frequency of 0.84 SNPs / 100 bp
Results of the tissue wise SNP and indel discovery are listed in Table 1 and Figure 1

Summary

Background

Ginger (Zingiber officinale) is a perennial plant in the family Zingiberaceae - its rhizome is commonly used as a cooking spice throughout the world. Singlepass sequencing of the 5' and/or 3' ends of randomly selected cDNA clones, is an effective approach to provide genetic information of an organism These sequences can serve as markers or tags for transcripts, and have been used in the development of SNP markers for reference genetic map and recovery of full-length cDNA and genomic sequences. We have categorized 38139 ESTs in to three tissue libraries leaves 13274, rhizomes 12763 and roots 12092 ESTs. In this study, we have categorized 38139 ESTs in to three tissue libraries leaves 13274, rhizomes 12763 and roots 12092 ESTs The availability of these EST sequences will allow comparative genomic studies between ginger and other monocotyledonous and dicotyledonous plants, development of molecular markers for the establishment of reference genetic map, design and construction of cDNA microarray for global gene expression profiling. The DNA substitution like transition (Ts) versus transversion (Tv) ratio of all the libraries in Ginger genome was calculated

Discussion

Conclusion:

References:

Results