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Functionally relevant microsatellites in sugarcane unigenes.

Swarup K Parida1, Awadhesh Pandit, Kishor Gaikwad

  • 1National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India.

BMC Plant Biology
|November 19, 2010
PubMed
Summary

Sugarcane unigenes contain microsatellites, offering insights into its complex genome. These microsatellites show high allelic diversity, proving useful for large-scale genotyping and understanding genetic variation.

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Area of Science:

  • Plant Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Unigene sequences are valuable resources for identifying functionally relevant microsatellites.
  • Understanding microsatellite distribution in sugarcane's complex genome is crucial.

Purpose of the Study:

  • To mine microsatellites from sugarcane unigenes.
  • To assess their in silico functional significance and allelic diversity.
  • To evaluate their utility in large-scale sugarcane genotyping.

Main Methods:

  • Bioinformatic mining of microsatellites in sugarcane unigene sequences.
  • In silico functional annotation of unigenes containing microsatellites.
  • Automated fragment analysis for allelic diversity assessment using fluorescently labeled primers.

Main Results:

  • Microsatellite repeats found in 4.92% of sugarcane unigenes, with GC-rich trinucleotides and GA-rich dinucleotides being most abundant.
  • Microsatellites identified within functional domains of 364 unigenes, including those encoding beta-amylase and protein kinase.
  • 726 allelic variants detected across 36 sugarcane genotypes, demonstrating primer utility for high-throughput genotyping.

Conclusions:

  • Microsatellite repeats are prevalent in sugarcane unigenes, with most having determined functions.
  • High allelic diversity in microsatellites, including those in functional protein domains, highlights their utility for analyzing variation in sugarcane's complex genome.