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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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High quality SNPs/Indels mining and characterization in ginger from ESTs data base.

Mahendra Gaur1, Aradhana Das1, Enketeswara Subudhi1

  • 1Centre of Biotechnology, Siksha 'O' Anushandhan University, Kalinga Nagar, Ghatikia, Bhubaneswar-751003, Odisha.

Bioinformation
|April 8, 2015
PubMed
Summary
This summary is machine-generated.

This study identified 8,810 high-quality single nucleotide polymorphisms (SNPs) in ginger (Zingiber officinale) using EST sequences. These genetic markers are valuable for future ginger genomic research and breeding programs.

Keywords:
ESTsGingerIndelsQualitySNPZingiber officinalein silico

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Area of Science:

  • Genomics
  • Plant Science
  • Biotechnology

Background:

  • Ginger (Zingiber officinale) is a widely used medicinal herb and spice.
  • Single nucleotide polymorphisms (SNPs) are crucial genetic markers for genomic analysis.
  • Existing public EST sequences often lack quality, hindering high-quality SNP detection.

Purpose of the Study:

  • To mine NCBI dbESTs for ginger EST sequences.
  • To identify and characterize high-quality SNPs and indels in ginger.
  • To provide a foundation for genetic studies and marker development in ginger.

Main Methods:

  • Mining NCBI dbESTs for 38,115 ginger EST sequences.
  • Assembling EST sequences into contigs using the CAP3 program.
  • Utilizing the QualitySNP software for high-quality SNP and indel detection.

Main Results:

  • Identified 11,523 potential SNPs, 8,810 high-quality SNPs, and 1,008 indels.
  • Determined an overall SNP frequency of 1.61 SNPs per 10 kbp.
  • Observed varying SNP and indel frequencies across different ginger tissues (rhizomes, leaves, roots).
  • Characterized 222 haplotypes, 2,355 exonic SNPs, 6,455 intronic SNPs, and 7,538 singletons.

Conclusions:

  • The study provides a valuable dataset of high-quality SNPs in ginger.
  • Detected SNPs can serve as effective markers for future genetic experiments and marker-assisted selection.
  • Tissue-specific analysis reveals differential SNP distribution, offering insights into ginger's genetic diversity.