EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance

Publication Overview
TitleEST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance
AuthorsKaur S, Cogan NOI, Stephens A, Noy D, Butsch M, Forster JW, Materne M
TypeJournal Article
Journal NameTheoretical and applied genetics
Volume127
Issue3
Year2014
Page(s)703-713
CitationKaur S, Cogan NOI, Stephens A, Noy D, Butsch M, Forster JW, Materne M. EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance. Theoretical and applied genetics. 2014; 127(3):703-713.

Abstract

KEY MESSAGE : Large-scale SNP discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. Lentil (Lens culinaris Medik.) is a highly nutritious food legume crop that is cultivated world-wide. Until recently, lentil has been considered a genomic ‘orphan’ crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. The present study reports on the identification of single-nucleotide polymorphisms (SNPs) from transcriptome sequencing data, utilisation of expressed sequence tag (EST)-derived simple sequence repeat (SSR) and SNP markers for construction of a gene-based genetic linkage map, and identification of markers in close linkage to major QTLs for tolerance to boron (B) toxicity. A total of 2,956 high-quality SNP markers were identified from a lentil EST database. Sub-sets of 546 SSRs and 768 SNPs were further used for genetic mapping of an intraspecific mapping population (Cassab� ×� ILL2024) that exhibits segregation for B tolerance. Comparative analysis of the lentil linkage map with the sequenced genomes of Medicago truncatula Gaertn., soybean (Glycine max [L.] Merr.) and Lotus japonicus L. indicated blocks of conserved macrosynteny, as well as a number of rearrangements. A single genomic region was found to be associated with variation for B tolerance in lentil, based on evaluation performed over 2� years. Comparison of flanking markers to genome sequences of model species (M. truncatula, soybean and Arabidopsis thaliana) identified candidate genes that are functionally associated with B tolerance, and could potentially be used for diagnostic marker development in lentil.
Features
This publication contains information about 770 features:
Feature NameUniquenameType
SNP_20005166SNP_20005166genetic_marker
SNP_20005182SNP_20005182genetic_marker
SNP_20005198SNP_20005198genetic_marker
SNP_20005327SNP_20005327genetic_marker
SNP_20005368SNP_20005368genetic_marker
SNP_20005402SNP_20005402genetic_marker
SNP_20005403SNP_20005403genetic_marker
SNP_20005416SNP_20005416genetic_marker
SNP_20005417SNP_20005417genetic_marker
SNP_20005468SNP_20005468genetic_marker
SNP_20005508SNP_20005508genetic_marker
SNP_20005542SNP_20005542genetic_marker
SNP_20005574SNP_20005574genetic_marker
SNP_20005575SNP_20005575genetic_marker
SNP_20005599SNP_20005599genetic_marker
SNP_20005652SNP_20005652genetic_marker
SNP_20005661SNP_20005661genetic_marker
SNP_20005684SNP_20005684genetic_marker
SNP_20005697SNP_20005697genetic_marker
SNP_20005721SNP_20005721genetic_marker
SNP_20005778SNP_20005778genetic_marker
SNP_20005830SNP_20005830genetic_marker
SNP_20005831SNP_20005831genetic_marker
SNP_20005832SNP_20005832genetic_marker
SNP_20005904SNP_20005904genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Lentil-Boron_tolerance-Kaur-2014
Featuremaps
This publication contains information about 1 maps:
Map Name
lentil-CassabxILL2024-F6
Stocks
This publication contains information about 2 stocks:
Stock NameUniquenameType
CassabCassabaccession
ILL2024ILL2024accession
Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2014
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s00122-013-2252-0
KeywordsArabidopsis thaliana, Glycine max, Lens culinaris, Lotus corniculatus var. japonicus, Medicago truncatula, boron, chromosome mapping, databases, expressed sequence tags, foods, genes, marker-assisted selection, microsatellite repeats, quantitative trait loci, single nucleotide polymorphism, soybeans, toxicity