Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

Nikolaj M. Vendelbo; Khalid Mahmood; Burkhard Steuernagel; Brande B.H. Wulff; Pernille Sarup; Mogens S. Hovmøller; Annemarie Fejer Justesen; Peter S. Kristensen; Jihad Orabi; Ahmed Jahoor

doi:10.3390/cells11081273

Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

Nikolaj M. Vendelbo^*, Khalid Mahmood, Burkhard Steuernagel, Brande B.H. Wulff, Pernille Sarup, Mogens S. Hovmøller, Annemarie Fejer Justesen, Peter S. Kristensen, Jihad Orabi, Ahmed Jahoor

^*Corresponding author for this work

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

11 Scopus citations

Abstract

The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.

Original language	English (US)
Article number	1273
Journal	Cells
Volume	11
Issue number	8
DOIs	https://doi.org/10.3390/cells11081273
State	Published - Apr 1 2022

Bibliographical note

Funding Information:
Funding: The research was funded by Innovation Fund Denmark (grant no. 8053-00085B), the Pajbjerg Foundation, the Danish Green Development and Demonstration Program (project Jr. NR. 34009-19-1603), and the Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat Cross-Institute Strategic Programme (BBS/E/J/000PR9780), and King Abdullah University of Science and Technology.

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

brown rust
genome-wide association study (GWAS)
k-mer
leaf rust
nucleotide-binding leucine-rich repeat (NLR)
Puccinia recondita f. sp. secalis
resistance gene enrichment sequencing (RenSeq)
Secale cereale L
single-molecule high-fidelity sequencing (HiFi)

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.3390/cells11081273

Cite this

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title = "Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics",

abstract = "The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent G{\"u}lzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio{\textregistered} long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.",

keywords = "brown rust, genome-wide association study (GWAS), k-mer, leaf rust, nucleotide-binding leucine-rich repeat (NLR), Puccinia recondita f. sp. secalis, resistance gene enrichment sequencing (RenSeq), Secale cereale L, single-molecule high-fidelity sequencing (HiFi)",

author = "Vendelbo, {Nikolaj M.} and Khalid Mahmood and Burkhard Steuernagel and Wulff, {Brande B.H.} and Pernille Sarup and Hovm{\o}ller, {Mogens S.} and Justesen, {Annemarie Fejer} and Kristensen, {Peter S.} and Jihad Orabi and Ahmed Jahoor",

note = "Funding Information: Funding: The research was funded by Innovation Fund Denmark (grant no. 8053-00085B), the Pajbjerg Foundation, the Danish Green Development and Demonstration Program (project Jr. NR. 34009-19-1603), and the Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat Cross-Institute Strategic Programme (BBS/E/J/000PR9780), and King Abdullah University of Science and Technology. Publisher Copyright: {\textcopyright} 2022 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2022",

month = apr,

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doi = "10.3390/cells11081273",

language = "English (US)",

volume = "11",

journal = "Cells",

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AU - Mahmood, Khalid

AU - Steuernagel, Burkhard

AU - Wulff, Brande B.H.

AU - Sarup, Pernille

AU - Hovmøller, Mogens S.

AU - Justesen, Annemarie Fejer

AU - Kristensen, Peter S.

AU - Orabi, Jihad

AU - Jahoor, Ahmed

N1 - Funding Information: Funding: The research was funded by Innovation Fund Denmark (grant no. 8053-00085B), the Pajbjerg Foundation, the Danish Green Development and Demonstration Program (project Jr. NR. 34009-19-1603), and the Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat Cross-Institute Strategic Programme (BBS/E/J/000PR9780), and King Abdullah University of Science and Technology. Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

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N2 - The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.

AB - The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.

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KW - leaf rust

KW - nucleotide-binding leucine-rich repeat (NLR)

KW - Puccinia recondita f. sp. secalis

KW - resistance gene enrichment sequencing (RenSeq)

KW - Secale cereale L

KW - single-molecule high-fidelity sequencing (HiFi)

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U2 - 10.3390/cells11081273

DO - 10.3390/cells11081273

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C2 - 35455953

AN - SCOPUS:85127907123

SN - 2073-4409

VL - 11

JO - Cells

JF - Cells

IS - 8

M1 - 1273

ER -

Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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