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

Overview
TitleAncient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil
AuthorsSharpe Andrew G, Ramsay Larissa, Sanderson Lacey-Anne, Fedoruk Michael J, Clarke Wayne E, Li Rong, Kagale Sateesh, Vijayan Perumal, Vandenberg Albert, Bett Kirstin E
TypeJournal Article
JournalBMC genomics
Volume14
DOI10.1186/1471-2164-14-192
eISSN1471-2164
Elocation10.1186/1471-2164-14-192
ISSN1471-2164
Journal AbbreviationBMC Genomics
Journal CountryEngland
LanguageEnglish
Language Abbreng
Publication Date2013
Publication ModelElectronic

Abstract

<p><b>BACKGROUND</b></br>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.</p><p><b>RESULTS</b></br>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.</p><p><b>CONCLUSIONS</b></br>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.</p>

Citation

Sharpe AG, Ramsay L, Sanderson LA, Fedoruk MJ, Clarke WE, Li R, Kagale S, Vijayan P, Vandenberg A, Bett KE. Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil. BMC genomics. 2013; 14:192.

Related Species
Related Species: 

Lentil (Lens culinaris Medik.) is an important pulse crop with annual production of 3-4 Mt across 70 countries (Cubero et al. 2009. DOI 10.1079/9781845934873.0000; pg. 13). Lentils are a good source of protein, carbohydrates, micronutrients and vitamins for human nutrition and is consumed in more than 120 countries. Furthermore, their small seed size and flat shape make them relatively quick cooking and easily decorticated compared to most other grain legumes (Sharpe et al. 2013. BMC Genomics. DOI 10.1186/1471-2164-14-192). The Lentil plant has a bushy growth habit with a height of about 40 cm; the seeds are lens-shaped and usually grow two per pod. ... [more]

 
Cross References
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DatabaseAccession
PMID: PubMedPMID:23506258
Research Area
Research Area: 
Breeding & Genetics

Plant breeding is the art and science of changing the traits of plants in order to produce desired characteristics. Plant breeding can be accomplished through many different techniques ranging from simply selecting plants with desirable characteristics for propagation, to more complex molecular techniques. ... [more]