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

TY - JOUR

T1 - Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

AU - Vendelbo, Nikolaj M.

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

PY - 2022/4

Y1 - 2022/4

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.

KW - brown rust

KW - genome-wide association study (GWAS)

KW - k-mer

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)

UR - http://www.scopus.com/inward/record.url?scp=85127907123&partnerID=8YFLogxK

U2 - 10.3390/cells11081273

DO - 10.3390/cells11081273

M3 - Journal article

C2 - 35455953

AN - SCOPUS:85127907123

VL - 11

JO - Cells

JF - Cells

IS - 8

M1 - 1273

ER -