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A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

Abstract

A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.

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Acknowledgments

Dr. Nils Stein and Dr. Marion Röder of the Institute of Plant Genetics and Crop Plant Research (IPK) are gratefully acknowledged for providing primer sequences of GBM- and GBMS- microsatellite markers. Dr. Patrick Hayes of the Oregon State University has sent us seeds of the 150 DH lines of the Steptoe × Morex population, which we greatly appreciate. We thank Dr. Patrick Schweizer of IPK for the gene expression analysis which permitted to identify defence genes in L94. We thank Truong M. Ta and Mumta Chhetri for assistance in mapping QTLs in the Steptoe × Morex population. We thank Benoit Gorguet, Fabien Marcel, Vincent Hennette, Simon Duquesne, Giorgia Albertazzi and Gonzalo R. Rodenas for marker analyses. We thank Dr. Joao Paulo for her help with the statistical analysis. We are grateful to Anton Vels of Unifarm, Wageningen University, for his technical support. This project was sponsored by the Dutch Organization for Scientific Research (NWO Aard- en Levenswetenschappen, project no. 809.36.001).

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Correspondence to R. E. Niks.

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Communicated by B. Keller.

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Marcel, T.C., Varshney, R.K., Barbieri, M. et al. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor Appl Genet 114, 487–500 (2007). https://doi.org/10.1007/s00122-006-0448-2

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Keywords

  • Quantitative Trait Locus
  • Double Haploid
  • Single Nucleotide Polymorphism
  • Recombinant Inbred Line Population
  • Amplify Fragment Length Polymorphism