title: Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.
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.
authors.forename: Cory D
authors.initials: CD
authors.lastname: Hirsch
authors.forename: Joseph
authors.initials: J
authors.lastname: Evans
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA
keywords: RNA-Seq; exome capture; genome diversity; re-sequencing