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

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  • Nikolaj M. Vendelbo, Nordic Seed A/S
  • ,
  • Khalid Mahmood, Nordic Seed A/S
  • ,
  • Burkhard Steuernagel, John Innes Centre
  • ,
  • Brande B.H. Wulff, John Innes Centre, King Abdullah University of Science and Technology
  • ,
  • Pernille Sarup, Nordic Seed A/S
  • ,
  • Mogens S. Hovmøller
  • Annemarie Fejer Justesen
  • Peter S. Kristensen
  • Jihad Orabi, Nordic Seed A/S
  • ,
  • Ahmed Jahoor, Nordic Seed A/S, Swedish University of Agricultural Sciences

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 languageEnglish
Article number1273
Number of pages21
Publication statusPublished - Apr 2022

Bibliographical note

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

    Research areas

  • 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)

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