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

Brief Funct Genomics. 2014 Jul;13(4):257-67. doi: 10.1093/bfgp/elt051. Epub 2014 Jan 6.


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.

Keywords: RNA-Seq; exome capture; genome diversity; re-sequencing.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA Copy Number Variations / genetics
  • Genome, Plant / genetics*
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA