Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes

Cory D. Hirsch, Joseph Evans, C. Robin Buell, Candice N. Hirsch

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

Abstract

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species.This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security.

Original languageEnglish (US)
Article numberelt051
Pages (from-to)257-267
Number of pages11
JournalBriefings in Functional Genomics and Proteomics
Volume13
Issue number4
DOIs
StatePublished - Jul 2014

Keywords

  • Exome capture
  • Genome diversity
  • RNA-Seq
  • Re-sequencing

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