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

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Abstract

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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.

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Acknowledgments

This work was supported by funding from the Victorian Department of Environment and Primary Industries and the Grains Research and Development Council, Australia.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments conducted in this study comply with current laws of Australia.

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Authors and Affiliations

  1. 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

    Sukhjiwan Kaur, Noel O. I. Cogan, Amber Stephens & John W. Forster

  2. Department of Environment and Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, VIC, 3401, Australia

    Dianne Noy, Mirella Butsch & Michael Materne

  3. La Trobe University, Bundoora, VIC, 3086, Australia

    John W. Forster

Authors
  1. Sukhjiwan Kaur
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  2. Noel O. I. Cogan
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  3. Amber Stephens
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  4. Dianne Noy
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  5. Mirella Butsch
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  6. John W. Forster
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  7. Michael Materne
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Corresponding author

Correspondence to John W. Forster.

Additional information

Communicated by A. J. Bervillé.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2013_2252_MOESM1_ESM.xlsx

ESM 1 Details of the 768plex SNP-OPA design: This file contains names and sequence information for all SNP markers used in linkage mapping (XLSX 239 kb)

122_2013_2252_MOESM2_ESM.xlsx

ESM 2 Details of all EST-SSR markers used in linkage mapping analysis: This file contains a list of all EST-SSR marker assays along with statistics on amplification efficiency and polymorphism rate (XLSX 36 kb)

122_2013_2252_MOESM3_ESM.xlsx

ESM 3 Linkage map statistics from the Cassab × ILL2024 RIL mapping population: This file contains details of different markers (SSRs and SNPs) and their corresponding positions on different LGs (XLSX 19 kb)

122_2013_2252_MOESM4_ESM.docx

ESM 4 Frequency distribution of B tolerance score: This file contains frequency histograms generated from phenotypic assessment of B tolerance from RILs of the mapping population (DOCX 146 kb)

122_2013_2252_MOESM5_ESM.pptx

ESM 5 Synteny between LGs of the Cassab × ILL2024 linkage map and chromosomes of M. truncatula: This file shows the visual representation of all LGs from Cassab x ILL2024 linkage map and their macrosyntenic relationships with the M. truncatula genome (PPTX 210 kb)

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Kaur, S., Cogan, N.O.I., Stephens, A. et al. EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance. Theor Appl Genet 127, 703–713 (2014). https://doi.org/10.1007/s00122-013-2252-0

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  • DOI: https://doi.org/10.1007/s00122-013-2252-0

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