title: Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil.
abstract: BACKGROUND
  The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model legume (Medicago truncatula). Lentil is a global food crop increasing in importance in the Indian sub-continent and elsewhere due to its nutritional value and quick cooking time. Despite this importance there has been a dearth of genetic and genomic resources for the crop and this has limited the application of marker-assisted selection strategies in breeding.
  
  
  RESULTS
  We describe here the development of a deep and diverse transcriptome resource for lentil using next generation sequencing technology. The generation of data in multiple cultivated (L. culinaris) and wild (L. ervoides) genotypes together with the utilization of a bioinformatics workflow enabled the identification of a large collection of SNPs and the subsequent development of a genotyping platform that was used to establish the first comprehensive genetic map of the L. culinaris genome. Extensive collinearity with M. truncatula was evident on the basis of sequence homology between mapped markers and the model genome and large translocations and inversions relative to M. truncatula were identified. An estimate for the time divergence of L. culinaris from L. ervoides and of both from M. truncatula was also calculated.
  
  
  CONCLUSIONS
  The availability of the genomic and derived molecular marker resources presented here will help change lentil breeding strategies and lead to increased genetic gain in the future.
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada. Andrew.Sharpe@nrc-cnrc.gc.ca
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
authors.forename: Larissa
authors.initials: L
authors.lastname: Ramsay
authors.forename: Lacey-Anne
authors.initials: LA
authors.lastname: Sanderson
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Fedoruk
authors.forename: Wayne E
authors.initials: WE
authors.lastname: Clarke
authors.forename: Rong
authors.initials: R
authors.lastname: Li
authors.forename: Sateesh
authors.initials: S
authors.lastname: Kagale
authors.forename: Perumal
authors.initials: P
authors.lastname: Vijayan
authors.forename: Albert
authors.initials: A
authors.lastname: Vandenberg
authors.forename: Kirstin E
authors.initials: KE
authors.lastname: Bett
mesh_terms: D008040:Genetic Linkage; D023281:Genomics; D005838:Genotype; D027806:Lens Plant / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA