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Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme

Abstract

The aim of this study was to convert existing faba bean (Vicia faba L.) single nucleotide polymorphism (SNP) markers from cleaved amplification polymorphic sequences and SNaPshot® formats, which are expensive and time-consuming, to the more convenient KBiosciences competitive allele‐specific PCR (KASP) assay format. Out of 80 assays designed, 75 were validated, though a core set of 67 of the most robust markers is recommended for further use. The 67 best KASP SNP assays were used across two generations of single seed descent to detect unintended outcrossing and to track and quantify loss of heterozygosity, a capability that will significantly increase the efficiency and performance of pure line production and maintenance. This same set of assays was also used to examine genetic relationships between the 67 members of the partly inbred panel, and should prove useful for line identification and diversity studies in the future.

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Abbreviations

CAPS:

Cleaved amplification polymorphic sequences

KASP:

KBiosciences competitive allele‐specific PCR

AFLP:

Amplified fragment length polymorphism

SSD:

Single seed descent

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Acknowledgments

This work has been supported by Defra as part of the Pulse Crop Genetic Improvement Network II (PCGINII) project. We thank Ken Street at ICARDA for identifying and donating seed of diverse genotypes from the ICARDA genebank, as well as Wolfgang Link (University of Göttingen), Mike Ambrose (JIC) and Gerard Duc (INRA-Dijon) for kind donations of seed from their respective germplasm collections. The full genotype dataset described here is available at http://www.viciatoolbox.org.

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Correspondence to D. M. O’Sullivan.

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Cottage, A., Gostkiewicz, K., Thomas, J.E. et al. Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme. Mol Breeding 30, 1799–1809 (2012). https://doi.org/10.1007/s11032-012-9745-4

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  • DOI: https://doi.org/10.1007/s11032-012-9745-4

Keywords

  • Vicia faba L.
  • KBiosciences competitive allele‐specific PCR (KASP)
  • Single nucleotide polymorphism (SNP)
  • Haplotype