Genome-Wide Association Study of Leaf Rust Resistance at Seedling and Adult Plant Stages in a Global Barley Panel

Abstract

Barley leaf rust caused by Puccinia hordei (Ph) is one of the major limiting biotic stresses of barley production worldwide and causes yield losses of up to 60%. A diversity panel of 316 barley genotypes (AM2017) composed of released cultivars, advanced breeding lines and landraces was screened for Ph resistance at the seedling stage using two isolates (SRT-SAT and SRT-MRC), while the adult plant stage resistance screening was conducted at the disease hotspot location of Sidi Allal Tazi (SAT) for the cropping seasons of 2017 and 2019. The phenotypic responses were combined with 36,793 single nucleotide polymorphism (SNP) markers in a genome-wide association study (GWAS) using the general linear model (GLM), mixed linear model (MLM), settlement of MLM under progressively exclusive relationship (SUPER), multiple-locus MLM (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) in GAPIT3, and MLM (K+Q), MLM (K+PCA), and GLM (Q) models in TASSEL to identify genomic regions linked to Ph resistance. Fourteen barley genotypes were resistant (R) at the seedling stage to both Ph isolates, SRT-SAT and SRT-MRC, and twelve genotypes were either resistant (R) or moderately resistant (MR) at the adult plant stage, whereas only one genotype was resistant at the seedling stage, and moderately resistant at the adult plant stage. The genome scan revealed 58 significant marker trait associations (MTA) among which 34 were associated with seedling resistance (SR) and 24 with adult plant resistance (APR). Common genomic regions conferring resistance to Ph were identified at both stages on chromosome 2H (106.53 cM and at 107.37 cM), and on chromosome 7H (126.7 cM). Among the 58 MTA identified, 26 loci had been reported in previous studies, while the remaining 32 loci were regarded as novel. Furthermore, the functional annotation of candidate genes (CGs) adjacent to 36 SNP markers with proteins involved in disease resistance further confirms that some of the SNP markers from our study could be associated with Ph resistance in barley. The resistant barley genotypes and some of the SNP markers from this study with high R2 and additive effects can be converted into high-throughput functional markers for accelerated selection and pyramiding of leaf rust resistance genes in North African barley germplasm.