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

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 t...

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Published in:	Theoretical and applied genetics Vol. 127; no. 3; pp. 703 - 713
Main Authors:	Kaur, Sukhjiwan, Cogan, Noel O. I, Stephens, Amber, Noy, Dianne, Butsch, Mirella, Forster, John W, Materne, Michael
Format:	Journal Article
Language:	English
Published:	Berlin/Heidelberg Springer-Verlag 01-03-2014 Springer Berlin Heidelberg Springer Springer Nature B.V
Subjects:	Agriculture Arabidopsis thaliana Barley Biochemistry Biocompatibility Biomedical and Life Sciences Biotechnology Boron Boron - toxicity Cereals Chromosome Mapping DNA, Plant - genetics Expressed Sequence Tags foods Genes Genes, Plant Genetic aspects Genetic Linkage Genomes Genomics Glycine max Legumes Lens culinaris Lens Plant - genetics Lentils Life Sciences Lotus corniculatus var. japonicus Lotus japonicus marker-assisted selection Medicago truncatula Medicago truncatula - genetics Microsatellite Repeats Original Paper Physiological aspects Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Polymorphism, Single Nucleotide Quantitative Trait Loci R&D Research & development Selection, Genetic single nucleotide polymorphism Single nucleotide polymorphisms soybeans Toxicity Transcriptome Australia Simple Interval Mapping Best Linear Unbiased Prediction Simple Sequence Repeat Marker Percentage Necrosis
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Summary:	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.
Bibliography:	http://dx.doi.org/10.1007/s00122-013-2252-0 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0040-5752 1432-2242
DOI:	10.1007/s00122-013-2252-0