Discovery of a Novel Leaf Rust (Puccinia recondita) Resistance Gene in Rye (Secale cereale L.) Using Association Genomics

Abstract

Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye.

Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping

“…Based on previous research findings [ 12 , 13 ] and taking into account that the inbred line JKI-NIL-Pr3 carried the Pr3 gene, we expected to identify one region on chromosome 1R with markers located around the NBS gene cluster. We detected two distinct QTLs in all four GWAS analyses performed; the first QTL was detected on 1RS, and the second QTL on 1RL, of chromosome 1R.…”

“…The results of the aforementioned studies were generated on the basis of interval mapping. Using a different approach, namely, genome-wide association study (GWAS; a strategy increasingly used for detection of resistance genes [ 11 ]), Vendelbo et al [ 12 , 13 ] mapped five LR resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL, and 7RS using Gülzow-based elite hybrid rye breeding germplasm. Two QTLs located on chromosome arms 1RS and 7RS were of particular importance.…”

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

“…The release of rye reference genome sequences (Lo7 and Weining) [ 6 , 7 ] has allowed researchers to conduct precise analyses at the molecular level. For example, Vendelbo et al [ 8 , 9 ] performed a genome-wide association study and mapped five LR resistance-associated quantitative trait loci (QTLs) on chromosome arms 1RS, 1RL, 2RL, 5RL, and 7RS; the two QTLs on chromosome arms 1RS and 7RS were especially important for LR resistance. The main resistance-associated marker on chromosome arm 1RS was physically co-localized with molecular markers delimiting the previously characterized Pr3 gene.…”

Genotype-specific expression of selected candidate genes conferring resistance to leaf rust of rye (Secale cereale L.)

“…Most of the Pr genes (Pr1-5, Pr-d-f, Pr-n, and Pr-r) confer resistance to a broad range of single-pustule isolates, with Pr1, Pr2, Pr-d, and Pr-r reportedly very useful for rye breeding (Roux et al, 2004). The recent publication of two rye genome sequences (Lo7 and Weining) (Li et al, 2021; Rabanus-Wallace et al, 2021) enabled Vendelbo et al (2021Vendelbo et al ( , 2022 to precisely characterise LR-related genes at the molecular level. Speci cally, ve LR resistance-associated quantitative trait loci (QTLs) were mapped on chromosome arms 1RS, 1RL, 2RL, 5RL, and 7RS on the basis of a genome-wide association study.…”