Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.)

Abstract

Powdery mildew is one of the most destructive diseases in the world, causing substantial grain yield losses and quality reduction in cereal crops. At present 23 powdery mildew resistance genes have been identified in rye, of which the majority are in wheat-rye translocation lines developed for wheat improvement. Here, we investigated the genetics underlying powdery mildew resistance in the Gülzow-type elite hybrid rye (Secale cereale L.) breeding germplasm. In total, 180 inbred breeding lines were genotyped using the state-of-the-art 600 K SNP array and phenotyped for infection type against three distinct field populations of B. graminis f. sp. secalis from Northern Germany (2013 and 2018) and Denmark (2020). We observed a moderate level of powdery mildew resistance in the non-restorer germplasm population, and by performing a genome-wide association study using 261,406 informative SNP markers, we identified a powdery mildew resistance locus, provisionally denoted PmNOS1, on the distal tip of chromosome arm 7RL. Using recent advances in rye genomic resources, we investigated whether nucleotide-binding leucine-rich repeat genes residing in the identified 17 Mbp block associated with PmNOS1 on recent reference genomes resembled known Pm genes.

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

“…Genotyping was done using a 600K SNP array with 600,843 SNP markers on a Affymetrix GeneTitan TM Scanner platform (Thermo Fisher Scientific Inc., Waltham, MA, USA) [ 47 ]. Marker map for the 600K SNP array on the Lo7 reference genome and evaluation of its performance in the assayed germplasm was recently presented in a study by Vendelbo et al [ 53 ]. The marker map was acquired from (Access date: 9 July 2021).…”

“…The leaf rust resistance-associated sites in the Weining reference genome were identified by the mapping of resistance-associated markers using the same procedure as described previously for the Lo7 reference genome. Nucleotide-binding leucine-rich repeat (NLR) genes residing in leaf rust resistance-associated regions in the Lo7 and Weining reference genomes were identified using the NLR annotation provided in a recent study by Vendelbo et al [ 53 ], available at (Access date: 9 July 2021). Coding sequences of potential candidate NLR genes were extracted using an online data repository [ 39 , 40 ].…”

“…The phylogenetic analysis was performed using NLR genes’ conserved NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins and CED-4) domain sequences. The NB-ARC sequences of NLR genes residing within the sites on the Lo7 and Weining reference genomes were extracted from the data repository file referred to above by Vendelbo et al [ 53 ]. The panel of known NLR-type R genes comprised leaf rust ( Lr1 , Lr10 , Lr21 , Lr22a ), stem rust ( Sr13 , Sr22 ) and yellow rust ( Yr5 , Yr10 , Yr28 ).…”

Single and multi‐trait genome‐wide association studies identify genomic regions associated with phenological traits in cowpea

“…The remaining confounding is accounted for by both, fixed effect model and the random effect model (Alemu et al., 2021). BLINK is a method like FarmCPU, using a multiple test for MLM that combines Bayesian information content, fixed effects model, and LD to enhance statistical power and reduce computational time (Vendelbo et al., 2021). The first six principal components (PCs) calculated using GAPIT were used as a covariate to account for the population structure, and Manhattan and Q – Q plots were generated using ggplot2 and qqman R package (R Core Team, 2020; Turner, 2018; Wickham, 2016).…”

Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

“…During the last decade alone, GWAS in barley has been successfully used for the identification of QTLs for abiotic stress tolerance [ 34 , 35 , 36 ], adaptation traits [ 37 , 38 , 39 ], yield-related traits [ 40 , 41 ], grain components and quality traits [ 42 , 43 , 44 ], and resistance to diseases [ 45 , 46 , 47 , 48 ]. Novel PM resistance QTLs have been identified using GWAS in wheat [ 49 , 50 ], oat [ 51 ], rye [ 52 ], and, of course, barley [ 53 , 54 , 55 , 56 ]. However, in Kazakhstan, no GWAS of barley resistance to local Bgh pathotypes has yet been attempted.…”