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Marker development and characterisation of Hordeum bulbosum introgression lines: a resource for barley improvement

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Abstract

A set of 110 diploid putative introgression lines (ILs) containing chromatin introgressed from the undomesticated species Hordeum bulbosum L. (bulbous barley grass) into cultivated barley (Hordeum vulgare L.) has been identified using a high-copy number retrotransposon-like PCR marker, pSc119.1, derived from rye (Secale cereale L.). To evaluate these lines, 92 EST-derived markers were developed by marker sequencing across four barley cultivars and four H. bulbosum genotypes. Single nucleotide polymorphisms and insertions/deletions conserved between the two species were then used to develop a set of fully informative cleaved amplified polymorphic sequence markers or size polymorphic insertion/deletion markers. Introgressed chromatin from H. bulbosum was confirmed and genetically located in 88 of these lines using 46 of the EST-derived PCR markers. A total of 96 individual introgressions were detected with most of them (94.8%) extending to the most distal marker for each respective chromosome arm. Introgressions were detected on all chromosome arms except chromosome 3HL. Interstitial or sub-distal introgressions also occurred, with two located on chromosome 2HL and one each on 3HS, 5HL and 6HS. Twenty-two putative ILs that were positive for H. bulbosum chromatin using pSc119.1 have not had introgressions detected with these single-locus markers. When all introgressions are combined, more than 36% of the barley genetic map has now been covered with introgressed chromatin from H. bulbosum. These ILs represent a significant germplasm resource for barley improvement that can be mined for diverse traits of interest to barley breeders and researchers.

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Acknowledgments

The authors would like to thank Professor Kazuhiro Sato for providing primer sequences of mapped EST markers, Mrs. Ruth Butler for statistical analysis of SNP frequencies and Dr. Samantha Baldwin for helping construct the figures for this manuscript. Comments from journal reviewers made a significant improvement to this manuscript.

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Authors and Affiliations

  1. New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand

    Paul A. Johnston, Gail M. Timmerman-Vaughan & Richard Pickering

  2. Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand

    Paul A. Johnston & Kevin J. F. Farnden

Authors
  1. Paul A. Johnston
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  2. Gail M. Timmerman-Vaughan
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  3. Kevin J. F. Farnden
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  4. Richard Pickering
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Corresponding author

Correspondence to Paul A. Johnston.

Additional information

Communicated by A. Graner.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2009_992_MOESM1_ESM.xls

Supplementary Table S1 A full list of the plant materials used in this study including information on pedigree, known traits derived from H. bulbosum and the chromosomal location of any detected introgressions (XLS 40 kb)

122_2009_992_MOESM2_ESM.xls

Supplementary Table S2 PCR primers and conditions for all the markers used in this study and including the diagnostic tools (restriction enzymes or size polymorphisms) used to discriminate between barley and H. bulbosum alleles. The restriction enzymes used for genetic mapping in the Steptoe x Morex population (Kleinhofs et al. 1993) are also included (XLS 59 kb)

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Johnston, P.A., Timmerman-Vaughan, G.M., Farnden, K.J.F. et al. Marker development and characterisation of Hordeum bulbosum introgression lines: a resource for barley improvement. Theor Appl Genet 118, 1429–1437 (2009). https://doi.org/10.1007/s00122-009-0992-7

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  • DOI: https://doi.org/10.1007/s00122-009-0992-7

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