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

Arumugam Chandrasekar¹, Aikkal Riju, Kandiyl Sithara

¹Bioinformatics centre, Indian Institute of spice research, P.B.No.1701, Marikunnu P.O, Calicut -673012, Kerala, India.

|March 4, 2010

Summary

Researchers identified over 64,000 Single Nucleotide Polymorphism (SNP) sites and 7,000 indel polymorphisms in ginger (Zingiber officinale) using expressed sequence tags. These molecular markers are valuable for ginger

Keywords:

Expressed Sequence Tag Ginger Indel SNPs Zingiber officinaleRosc in silico

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Area of Science:

* Botany and Plant Science
* Molecular Biology and Genetics

Background:

* Ginger (Zingiber officinale) is a widely recognized spice and medicinal plant.
* Expressed Sequence Tags (ESTs) are valuable resources for genetic discovery.
* High-throughput methods enable efficient detection of Single Nucleotide Polymorphisms (SNPs) and indels.

Purpose of the Study:

* To mine ginger EST sequences for identifying SNPs and indel polymorphisms.
* To characterize the frequency and distribution of these genetic variations.
* To assess the utility of identified variations as molecular markers for ginger genetics.

Main Methods:

* Mining of 38,139 ginger EST sequences from NCBI dbEST.
* Assembly of EST sequences into contigs using the CAP3 program.
* Detection of candidate SNPs and indel polymorphisms using the AutoSNP program.

Main Results:

* Identification of 64,026 SNP sites and 7,034 indel polymorphisms.
* Overall frequency of 0.84 SNPs/indels per 100 bp.
* Higher SNP/indel frequency observed in rhizomes (1.08/100 bp) compared to leaves (0.63/100 bp) and roots (0.82/100 bp).
* Transversion mutations were more frequent than transitions in detected SNPs.

Conclusions:

* The study successfully identified a substantial number of SNPs and indels in ginger.
* These identified genetic variations serve as valuable molecular markers for ginger genetic studies.
* The findings contribute to a better understanding of ginger genetic diversity.