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Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79

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A Correction to this article was published on 01 September 2018

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Abstract

Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs.

Abstract

Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.

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  • 01 September 2018

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Acknowledgements

This research was funded, in part, by the Triticeae Coordinated Agricultural Project (2011-68002-30029) from the United States Department of Agriculture National Institute of Food and Agriculture, the Lieberman-Okinow Endowment at the University of Minnesota, American Malting Barley Association, and United States Department of Agriculture-Agricultural Research Service Cooperative Agreement 58-5062-5-012 (Understanding Stem Rust Resistance in Barley and Germplasm). AJC acknowledges financial support from the following University of Minnesota fellowships: Norman E. Borlaug Graduate Fellowship for International Agriculture supported by the Vaale-Henry Endowment, the Minnesota Discovery, Research, and Innovation (MnDRIVE) Fellowship, and the Doctoral Dissertation Fellowship. We thank T. Szinyei and M. Martin, for excellent technical assistance, and Dr. Ahmad Sallam and Dr. María Muñoz-Amatriaín for assistance data analysis.

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Authors and Affiliations

  1. Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA

    Austin J. Case & Brian J. Steffenson

  2. Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya

    Sridhar Bhavani

  3. Kenya Agriculture and Livestock Research Organization (KALRO), Njoro, Kenya

    Godwin Macharia

  4. Department of Plant Sciences, University of the Free State, Bloemfontein, Republic of South Africa

    Zacharias Pretorius

  5. Pannar Seed (Pyt) Ltd, Greytown, Republic of South Africa

    Vicky Coetzee & Frederik Kloppers

  6. Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA

    Priyanka Tyagi

  7. USDA-ARS, Raleigh, NC, 27695, USA

    Gina Brown-Guedira

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  1. Austin J. Case
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Correspondence to Brian J. Steffenson.

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Additional information

Communicated by Frank Ordon.

The author name Frederik Kloppers was incorrect in original publication. It has been corrected.

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Online Resource 1

Hietpas-5/Hiproly and PI 382313/Hiproly recombinant inbred line population subsets used for genotyping and phenotyping and those used for genotyping only. In the Hietpas-5/Hiproly and the PI 382313/Hiproly populations, 280 and 278 RILs were genotyped, respectively, but only 200 RILs of each population were used in phenotyping. (XLSX 47 kb)

Online Resource 2

Hietpas-5/Hiproly recombinant inbred line population raw genotyping-by-sequencing calls. Raw SNP data were generated as described in Materials and Methods section where marker_new, Chrom_new, and Pos_new are based on the updated genome assembly. Ref_seq is 30 bp before and 30 bp after the SNP in this reference genome version, whereas Marker_old, Chrom_old, and Pos_old were based on an older version of the reference genome where chromosomes were split into two parts. (CSV 14416 kb)

Online Resource 3

PI 382313/Hiproly recombinant inbred line population raw genotyping-by-sequencing calls. Raw SNP data were generated as described in Materials and Methods section where marker_new, Chrom_new, and Pos_new are based on the updated genome assembly. Ref_seq is 30 bp before and 30 bp after the SNP in this reference genome version, whereas Marker_old, Chrom_old, and Pos_old were based on an older version of the reference genome where chromosomes were split into two parts. (CSV 10693 kb)

Online Resource 4

Hietpas-5/Hiproly recombinant inbred line population imputed genotyping-by-sequencing calls to fill in missing genotype data. Raw genotype-by-sequencing calls were imputed using the LinkImpute method as described in Materials and Methods section (Money et al. 2015). (CSV 12503 kb)

Online Resource 5

PI 382313/Hiproly recombinant inbred line population imputed genotyping-by-sequencing calls to fill in missing genotype data. Raw genotype-by-sequencing calls were imputed using the LinkImpute method as described in Materials and Methods section (Money et al. 2015). (CSV 9266 kb)

Online Resource 6

Hietpas-5/Hiproly recombinant inbred line population final genotyping-by-sequencing calls after imputation and filtering. The final set of genotype-by-sequencing marker calls were first imputed and then filtered for quality control as described in Materials and Methods section. The total number of markers was 8586, including the two morphological markers. Alleles calls were converted to A, B, H, and N calls, where “A” alleles were Hietpas-5-like, “B” alleles Hiproly-like, “H” was heterozygous, and “N” was missing. (CSV 5244 kb)

Online Resource 7

PI 382313/Hiproly recombinant inbred line population final genotyping-by-sequencing calls after imputation and filtering. The final set of genotype-by-sequencing marker calls were first imputed and then filtered for quality control as described in Materials and Methods section. The total number of markers remaining was 6985, including two morphological markers. Alleles calls were converted to A, B, H, and N calls, where “A” alleles were PI 382313-like, “B” alleles Hiproly-like, “H” was heterozygous, and “N” was missing. (CSV 4239 kb)

Online Resource 8

Linkage maps of the Hietpas-5/Hiproly and PI 382313/Hiproly recombinant inbred line populations. Marker cM distance was calculated as described in Materials and Methods section. Maps were constructed with 1585 markers in the Hietpas-5/Hiproly population and 1364 in the PI 382313/Hiproly population. (CSV 165 kb)

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Case, A.J., Bhavani, S., Macharia, G. et al. Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79. Theor Appl Genet 131, 2245–2266 (2018). https://doi.org/10.1007/s00122-018-3149-8

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  • DOI: https://doi.org/10.1007/s00122-018-3149-8

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