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 Gulzow 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 (R) 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

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

Published in

Cells
2022, volume: 11, number: 8, article number: 1273
Publisher: MDPI

SLU Authors

• Jahoor, Ahmed

  • Department of Plant Breeding, Swedish University of Agricultural Sciences
    
  • Nordic Seed A/S

Associated SLU-program

SLU Plant Protection Network

UKÄ Subject classification

Agricultural Science

Publication identifier

• DOI: https://doi.org/10.3390/cells11081273

Permanent link to this page (URI)

https://res.slu.se/id/publ/117088