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- Title
EST-SNP discovery and dense genetic mapping in lentil ( Lens culinaris Medik.) enable candidate gene selection for boron tolerance.
- Authors
Kaur, Sukhjiwan; Cogan, Noel; Stephens, Amber; Noy, Dianne; Butsch, Mirella; Forster, John; Materne, Michael
- 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. Abstract: 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.
- Subjects
SINGLE nucleotide polymorphisms; PLANT gene mapping; LENTILS; PLANT genes; BORON; COMPARATIVE studies
- Publication
Theoretical & Applied Genetics, 2014, Vol 127, Issue 3, p703
- ISSN
0040-5752
- Publication type
Article
- DOI
10.1007/s00122-013-2252-0