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Open Access Highly Accessed Research article

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

Andrew G Sharpe1*, Larissa Ramsay1, Lacey-Anne Sanderson2, Michael J Fedoruk2, Wayne E Clarke3, Rong Li1, Sateesh Kagale1, Perumal Vijayan2, Albert Vandenberg2 and Kirstin E Bett2*

Author Affiliations

1 National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

2 Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada

3 Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Pl., Saskatoon, SK, S7N 0X2, Canada

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BMC Genomics 2013, 14:192  doi:10.1186/1471-2164-14-192

Published: 18 March 2013

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.