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

Publication Overview
TitleAncient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil
AuthorsSharpe AG, Ramsay L, Sanderson LA, Fedoruk MJ, Clarke WE, Li R, Kagale S, Vijayan P, Vandenberg A, Bett KE
TypeJournal Article
Journal NameBMC genomics
Volume14
Year2013
Page(s)192
CitationSharpe 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.

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.

Features
This publication contains information about 44,943 features:
Feature NameUniquenameType
LcC00556p1106LcC00556p1106genetic_marker
LcC00556p1191LcC00556p1191genetic_marker
LcC00556p1233LcC00556p1233genetic_marker
LcC00556p1278LcC00556p1278genetic_marker
LcC00556p1386LcC00556p1386genetic_marker
LcC00556p1424LcC00556p1424genetic_marker
LcC00556p457LcC00556p457genetic_marker
LcC00556p501LcC00556p501genetic_marker
LcC00556p517LcC00556p517genetic_marker
LcC00556p577LcC00556p577genetic_marker
LcC00556p694LcC00556p694genetic_marker
LcC00556p863LcC00556p863genetic_marker
LcC00556p969LcC00556p969genetic_marker
LcC00557p655LcC00557p655genetic_marker
LcC00557p658LcC00557p658genetic_marker
LcC00557p667LcC00557p667genetic_marker
LcC00557p695LcC00557p695genetic_marker
LcC00557p723LcC00557p723genetic_marker
LcC00558p100LcC00558p100genetic_marker
LcC00558p101LcC00558p101genetic_marker
LcC00558p275LcC00558p275genetic_marker
LcC00558p277LcC00558p277genetic_marker
LcC00559p468LcC00559p468genetic_marker
LcC00560p210LcC00560p210genetic_marker
LcC00560p246LcC00560p246genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
lentil-CDCRobinx964a-46-RIL
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2013
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-14-192
Elocation10.1186/1471-2164-14-192
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
LanguageEnglish
Publication TypeResearch Support, Non-U.S. Gov't