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Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton.

Armel Salmon1, Joshua A Udall, Jeffrey A Jeddeloh

  • 1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.

G3 (Bethesda, Md.)
|August 22, 2012
PubMed
Summary

Targeted sequence capture efficiently sequences homeologs in polyploid cotton, enabling cost-effective genomic studies. This method is scalable for diverse research in complex plant genomes.

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Area of Science:

  • Genomics
  • Plant Biology
  • Molecular Biology

Background:

  • Targeted sequence capture offers efficient and cost-effective sequencing of specific genomic regions.
  • Polyploid genomes, like that of cotton (Gossypium hirsutum), present unique challenges for genetic analysis.
  • Understanding homeologs in polyploids is crucial for crop improvement and evolutionary studies.

Purpose of the Study:

  • To demonstrate the feasibility of targeted sequence capture for enriching and sequencing homeologs in polyploid cotton.
  • To develop custom probes for capturing specific gene pairs in Gossypium hirsutum.
  • To assess capture efficiency and analyze heterozygosity in wild and domesticated cotton.

Main Methods:

  • Design of custom hybridization probes targeting 1000 genes (500 homeolog pairs) from the cotton transcriptome.
Keywords:
Gossypiumallopolyploidyhomoeologsnext-generation sequencingsequence capture

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  • Application of NimbleGen capture arrays for targeted enrichment in two divergent Gossypium hirsutum samples.
  • Sequencing of captured regions and analysis of capture efficiency and heterozygosity.

    • Main Results:

    • Efficient capture of both homeologs in the allopolyploid cotton nucleus with high coverage.
    • Consistent capture efficiency across different accessions and sample multiplexing.
    • Identification of low intraindividual heterozygosity, with asymmetrical levels observed in cultivated cotton.

    Conclusions:

    • Targeted sequence capture is a viable and efficient method for studying polyploid genomes, specifically in cotton.
    • The approach is scalable and adaptable for various research questions involving polyploid plants.
    • Findings provide insights into cotton genome structure and domestication impacts on heterozygosity.