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Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)

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Abstract

Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT®) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1–4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar® markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar® assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM–ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.

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Acknowledgments

Research supported by the “AGER-Agroalimentare e Ricerca” foundation, “From Seed to Pasta” project, and by Emilia-Romagna Region (Laboratorio SITEIA, Misura 4 “Sviluppo di rete”, Azione A). The Interdepartmental Centre for Biotechnology (University of Bologna, Italy) is gratefully acknowledged. The authors thank S. Corneti and S. Stefanelli for technical assistance in molecular genotyping and phenotyping, J. Číhalíková, R. Šperková, and Z. Dubská in chromosome sorting and preparation of amplified chromosomal DNA. F.M. Bassi was supported by program “Master and Back” of the Regione Autonoma della Sardegna, and by Monsanto Beachell-Borlaug International Scholarship.

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Authors and Affiliations

  1. Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, Bologna, 40127, Italy

    Irma Terracciano, Marco Maccaferri, Filippo Bassi, Paola Mantovani, Maria C. Sanguineti, Silvio Salvi & Roberto Tuberosa

  2. Department of Plant Sciences, North Dakota State University, 166 N. Bolley Dr, Fargo, ND, 58102, USA

    Filippo Bassi

  3. Società Produttori Sementi Bologna, Via Macero 1, Argelato, Bologna, 40050, Italy

    Paola Mantovani & Andrea Massi

  4. Institute of Experimental Botany, Sokolovska 6, 77200, Olomouc, Czech Republic

    Hana Šimková & Jaroslav Doležel

  5. CIMMYT, Carretera Mexico-Veracruz KM. 45, 56130, Texcoco, Mexico

    Karim Ammar

  6. Cereal Disease Laboratory, Agricultural Research Service, US Department of Agriculture, 1551 Lindig Avenue, St. Paul, MN, 55108, USA

    James Kolmer

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  1. Irma Terracciano
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Correspondence to Marco Maccaferri.

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Terracciano, I., Maccaferri, M., Bassi, F. et al. Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.). Theor Appl Genet 126, 1077–1101 (2013). https://doi.org/10.1007/s00122-012-2038-9

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