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

Irma Terracciano; Marco Maccaferri; Filippo Bassi; Paola Mantovani; Maria C. Sanguineti; Silvio Salvi; Hana Šimková; Jaroslav Doležel; Andrea Massi; Karim Ammar; James Kolmer; Roberto Tuberosa

doi:10.1007/s00122-012-2038-9

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

Irma Terracciano, Marco Maccaferri, Filippo Bassi, Paola Mantovani, Maria C. Sanguineti, Silvio Salvi, Hana Šimková, Jaroslav Doležel, Andrea Massi, Karim Ammar, James Kolmer, Roberto Tuberosa

Plant Pathology

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1077-1101
Number of pages	25
Journal	Theoretical and Applied Genetics
Volume	126
Issue number	4
DOIs	https://doi.org/10.1007/s00122-012-2038-9
State	Published - Apr 2013

Bibliographical note

Funding Information:
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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Terracciano, I., Maccaferri, M., Bassi, F., Mantovani, P., Sanguineti, M. C., Salvi, S., Šimková, H., Doležel, J., Massi, A., Ammar, K., Kolmer, J., & Tuberosa, R. (2013). Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.). Theoretical and Applied Genetics, 126(4), 1077-1101. https://doi.org/10.1007/s00122-012-2038-9

Terracciano, I, Maccaferri, M, Bassi, F, Mantovani, P, Sanguineti, MC, Salvi, S, Šimková, H, Doležel, J, Massi, A, Ammar, K, Kolmer, J & Tuberosa, R 2013, 'Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)', Theoretical and Applied Genetics, vol. 126, no. 4, pp. 1077-1101. https://doi.org/10.1007/s00122-012-2038-9

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

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{\textregistered}) 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{\textregistered} markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar{\textregistered} 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.",

author = "Irma Terracciano and Marco Maccaferri and Filippo Bassi and Paola Mantovani and Sanguineti, \{Maria C.\} and Silvio Salvi and Hana {\v S}imkov{\'a} and Jaroslav Dole{\v z}el and Andrea Massi and Karim Ammar and James Kolmer and Roberto Tuberosa",

note = "Funding Information: 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. {\v C}{\'i}hal{\'i}kov{\'a}, R. {\v S}perkov{\'a}, and Z. Dubsk{\'a} 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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doi = "10.1007/s00122-012-2038-9",

language = "English (US)",

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T1 - Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)

AU - Terracciano, Irma

AU - Maccaferri, Marco

AU - Bassi, Filippo

AU - Mantovani, Paola

AU - Sanguineti, Maria C.

AU - Salvi, Silvio

AU - Šimková, Hana

AU - Doležel, Jaroslav

AU - Massi, Andrea

AU - Ammar, Karim

AU - Kolmer, James

AU - Tuberosa, Roberto

N1 - Funding Information: 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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N2 - 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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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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