Multi-Location Evaluation of Global Wheat Lines Reveal Multiple QTL for Adult Plant Resistance to Septoria Nodorum Blotch (SNB) Detected in Specific Environments and in Response to Different Isolates

Abstract

The slow rate of genetic gain for improving resistance to Septoria nodorum blotch (SNB) is due to the inherent complex interactions between host, isolates, and environments. Breeding for improved SNB resistance requires evaluation and selection of wheat genotypes consistently expressing low SNB response in different target production environments. The study focused on evaluating 232 genotypes from global origins for resistance to SNB in the flag leaf expressed in different Western Australian environments. The aim was to identify resistant donor germplasm against historical and contemporary pathogen isolates and enhance our knowledge of the genetic basis of genotype-byenvironment interactions for SNB response. Australian wheat varieties, inbred lines from Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), and International Center for Agricultural Research in the Dry Areas (ICARDA), and landraces from discrete regions of the world showed low to moderate phenotypic correlation for disease response amongst genotypes when evaluated with historical and contemporary isolates at two locations across 3 years in Western Australia (WA). Significant (P < 0.001) genotype-by-environment interactions were detected regardless of same or different isolates used as an inoculum source. Joint regression analysis identified 19 genotypes that consistently expressed low disease severity under infection with different isolates in multi-locations. The CIMMYT inbred lines, 30ZJN09 and ZJN12 Qno25, were particularly pertinent as they had low SNB response and highest trait stability at two locations across 3 years. Genome wide association studies detected 20 QTL associated with SNB resistance on chromosomes 1A, 1B, 4B, 5A, 5B, 6A, 7A, 7B, and 7D. QTL on chromosomes 1B and 5B were previously reported in similar genomic regions. Multiple QTL were identified on 1B, 5B, 6A, and 5A and detected in response to SNB infection against different isolates and specific environments. Known SnTox-Snn interactions were either not evident or variable across WA environments and SNB response may involve other multiple complex biological mechanisms.

Identification and cross-validation of genetic loci conferring resistance to Septoria nodorum blotch using a German multi-founder winter wheat population

“…Given the discriminatory nature of this SNP in our eight founders, these results highlight the potential of this marker for application in marker-assisted selection. Two adult plant SNB resistance/susceptibility QTL have previously been reported on chromosome 5A (Friesen et al 2009 ; Francki et al 2020 ) (Table S3). Of these, our SNB QTL QSnb.nmbu-5A.1 (558.7–571.7 Mb) overlaps with the location of a locus conferring resistance/susceptibility to SNB in the bi-parental population BR34 × Grandin (~ 558.340 Mb) (Friesen et al 2009 ).…”

“…Given the discriminatory nature of this SNP in our eight founders, these results highlight the potential of this marker for application in marker-assisted selection. Two adult plant SNB resistance/susceptibility QTL have previously been reported on chromosome 5A (Friesen et al 2009;Francki et al 2020) (Table S3). Of these, our SNB QTL QSnb.…”

“…Subsequent reduction of the ToxA sensitive wheat growing area by 13.5% between 2009 and 2013 was estimated to have saved 50 million $ in crop losses (Vleeshouwers and Oliver 2014 ). Genetic studies have identified numerous additional SNB resistance QTLs at the juvenile or the adult plant stages (reviewed most recently by Ruud and Lillemo 2018 , with additional QTL identified in subsequent studies by Czembor et al 2019 ; Francki et al 2020 ; Hu et al 2019 ; Lin et al 2020a ; Ruud et al 2019 ), including many that have not been associated with genetic loci controlling effector sensitivity. Taken together, these map to 20 of the 21 wheat chromosomes.…”

Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize

“…GWAS is based on diversity panels and takes advantage from historic recombination events. Thus, much more accessions are screened with the possibility to identify new alleles not represented in parents of bi-parental mapping populations [ 20 ]. The outcome of a GWAS is mainly dependent on population size, but also on the crop- and genome-specific linkage disequilibrium (LD) between marker and phenotype.…”

“…The genetic control of resistance to SNB is also very complex, consisting of many loci with additively inherited minor effects and prone to high genotype × environment interactions resulting in only low to moderate correlations among environments [ 20 , 66 ]. Therefore, only a few QTLs have been detected across environments (locations, years).…”