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.
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
CassabCassabbreeding_research_material
ILL2024ILL2024breeding_research_material
Cassab × ILL2024Cassab × ILL2024population
Features
This publication contains information about 768 features:
Feature NameUniquenameType
SNP_20000010SNP_20000010genetic_marker
SNP_20000037SNP_20000037genetic_marker
SNP_20000104SNP_20000104genetic_marker
SNP_20000105SNP_20000105genetic_marker
SNP_20000149SNP_20000149genetic_marker
SNP_20000150SNP_20000150genetic_marker
SNP_20000164SNP_20000164genetic_marker
SNP_20000192SNP_20000192genetic_marker
SNP_20000219SNP_20000219genetic_marker
SNP_20000221SNP_20000221genetic_marker
SNP_20000222SNP_20000222genetic_marker
SNP_20000246SNP_20000246genetic_marker
SNP_20000247SNP_20000247genetic_marker
SNP_20000248SNP_20000248genetic_marker
SNP_20000270SNP_20000270genetic_marker
SNP_20000273SNP_20000273genetic_marker
SNP_20000283SNP_20000283genetic_marker
SNP_20000286SNP_20000286genetic_marker
SNP_20000299SNP_20000299genetic_marker
SNP_20000300SNP_20000300genetic_marker
SNP_20000301SNP_20000301genetic_marker
SNP_20000302SNP_20000302genetic_marker
SNP_20000305SNP_20000305genetic_marker
SNP_20000308SNP_20000308genetic_marker
SNP_20000309SNP_20000309genetic_marker

Pages

Featuremaps
This publication contains information about 2 maps:
Map Name
lentil-CassabxILL2024-F6
Lentil-Cassab_×_ILL2024-RIL-2014
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
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4785701