title: EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance.
abstract: 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.
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, VIC, 3083, Australia.
authors.forename: Sukhjiwan
authors.initials: S
authors.lastname: Kaur
authors.forename: Noel O I
authors.initials: NO
authors.lastname: Cogan
authors.forename: Amber
authors.initials: A
authors.lastname: Stephens
authors.forename: Dianne
authors.initials: D
authors.lastname: Noy
authors.forename: Mirella
authors.initials: M
authors.lastname: Butsch
authors.forename: John W
authors.initials: JW
authors.lastname: Forster
authors.forename: Michael
authors.initials: M
authors.lastname: Materne
mesh_terms: D001895:Boron / Q000633:toxicity*; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D008040:Genetic Linkage; D023281:Genomics; D027806:Lens Plant / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D059467:Transcriptome
chemical_list: D018744:DNA, Plant; D001895:Boron