Ancient orphan crop joins modern era: Gene-based SNP discovery and mapping in lentil

  1. Get@NRC: Ancient orphan crop joins modern era: Gene-based SNP discovery and mapping in lentil (Opens in a new window)
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Journal titleBMC Genomics
Article number192
Subjectcomplementary DNA; molecular marker; transcriptome; 3' untranslated region; article; barrel medic; bioinformatics; chromosome inversion; chromosome translocation; computer model; controlled study; crop; cultivated species; gene locus; gene mapping; genetic identification; genetic linkage; genotype; Lens ervoides; lentil; nonhuman; plant genome; sequence analysis; sequence homology; single nucleotide polymorphism; transcriptomics; wild plant; Genetic Linkage; Genomics; Genotype; Lens Plant; Medicago truncatula; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Cicer arietinum; Lens (angiosperm); Lens culinaris; Lens ervoides; Medicago truncatula; Papilionoideae; Pisum sativum
AbstractBackground: 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. © 2013 Sharpe et al.; licensee BioMed Central Ltd.
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AffiliationNational Research Council Canada (NRC-CNRC)
Peer reviewedYes
NPARC number21270672
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Record identifierf46f5998-b20d-442f-91be-94ea67cdafc3
Record created2014-02-17
Record modified2016-05-09
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