Association Mapping of Seedling Resistance to Spot Form Net Blotch in a Worldwide Collection of Barley

Abstract

Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata, is an important foliar disease of barley in major production regions around the world. Deployment of adequate host resistance is challenging because the virulence of P. teres f. maculata is highly variable and characterized minor-effect resistances are typically ineffective against the diverse pathogen populations. A world barley core collection consisting of 2,062 barley accessions of diverse origin and genotype were phenotyped at the seedling stage with four P. teres f. maculata isolates collected from the United States (FGO), New Zealand (NZKF2), Australia (SG1), and Denmark (DEN 2.6). Of the 2,062 barley accessions phenotyped, 1,480 were genotyped with the Illumina barley iSelect chip and passed the quality controls with 5,954 polymorphic markers used for further association mapping analysis. Genome-wide association mapping was utilized to identify and map resistance loci from the seedling disease response data and the single nucleotide polymorphism (SNP) marker data. The best among six different regression models was identified for each isolate and association analysis was performed separately for each. A total of 138 significant (-log10P value>3.0) marker-trait associations (MTA) were detected. Using a 5 cM cutoff, a total of 10, 8, 13, and 10 quantitative trait loci (QTL) associated with SFNB resistance were identified for the FGO, SG1, NZKF2, and DEN 2.6 isolates, respectively. Loci containing from 1 to 34 MTA were identified on all seven barley chromosomes with one locus at 66 to 69 cM on chromosome 2H common to all four isolates. Six distinct loci were identified by the association mapping (AM) analysis that corresponded to previously characterized SFNB resistance QTL identified by biparental population analysis (QRpt4, QRpt6, Rpt4, Rpt6, Rpt7, and a QTL on 4H that was not given a provisional gene or QTL nomenclature). The 21 putative novel loci identified may represent a broad spectrum of resistance and or susceptibility loci. This is the first comprehensive AM study to characterize SFNB resistance loci underlying broad populations of the barley host and P. teres f. maculata pathogen.

Mapping of quantitative trait loci associated with resistance to net form net blotch (Pyrenophora teres f. teres) in a doubled haploid Norwegian barley population

“…Tamang et al identified markers at 53.7–59.2 cM (consensus map) on chromosome 4H associated with seedling resistance against the two SFNB isolates NZKF2 and DEN.2 from New Zealand and Denmark, respectively, and this region co-locates with AL_QRptt4-1 found in this study [26]. One of the markers significantly associated with resistance to NZKF2 and DEN2.6 is also present in the AxL linkage map and showed significant association with seedling resistance to 6949B.…”

SNPs associated with barley resistance to isolates of Pyrenophora teres f. teres

“…The pathogen exists in two forms based on the symptoms they cause: the net form of net blotch (P. teres f. teres) and the spot form of net blotch (P. teres f. maculata). The net form of net blotch (NFNB) is the dominant form in different regions of Russia; the spot form of net blotch (SFNB) was found only in the southern part of European Russia [1]. NFNB epidemics in Northwest Russia appear with a frequency of 5 times every 10 years [2].…”

Characterizing the Pyrenophora teres f. maculata–Barley Interaction Using Pathogen Genetics

“…More recently, genome-wide association studies (GWAS) have been used to identify genomic regions associated with resistance/susceptibility. Tamang et al (2015) used SFNB disease reaction data ( Neupane et al 2015 ) and genotypic data ( Muñoz-Amatriaín et al 2014 ) from a 1480-line barley core collection to identify 27 distinct loci associated with SFNB resistance/susceptibility. Among the 27 loci identified in GWAS, six loci were consistent with previously identified QTL ( Tamang et al 2015 ).…”

“… Tamang et al (2015) used SFNB disease reaction data ( Neupane et al 2015 ) and genotypic data ( Muñoz-Amatriaín et al 2014 ) from a 1480-line barley core collection to identify 27 distinct loci associated with SFNB resistance/susceptibility. Among the 27 loci identified in GWAS, six loci were consistent with previously identified QTL ( Tamang et al 2015 ). Similarly, Wang et al (2015) identified 29 marker trait associations (MTA) that represented 24 unique regions among 898 breeding lines from the Northern Region Barley Breeding Program in Australia.…”