Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed.

Key message: High genetic variation in two European maize landraces can be harnessed to improve Gibberella ear rot resistance by integrated genomic tools. Fusarium graminearum(Fg) causes Gibberella ear rot (GER) in maize leading to yield reduction and contamination of grains with several mycotoxins. This study aimed to elucidate the molecular basis of GER resistance among 500 doubled haploid lines derived from two European maize landraces, “Kemater Landmais Gelb” (KE) and “Petkuser Ferdinand Rot” (PE). The two landraces were analyzed individually using genome-wide association studies and genomic selection (GS). The lines were genotyped with a 600-k maize array and phenotyped for GER severity, days to silking, plant height, and seed-set in four environments using artificial infection with a highly aggressive Fg isolate. High genotypic variances and broad-sense heritabilities were found for all traits. Genotype-environment interaction was important throughout. The phenotypic (r) and genotypic ( $${r}_{g}$$rg ) correlations between GER severity and three agronomic traits were low (r = − 0.27 to 0.20; $${r}_{g}\hspace{0.17em}$$rg = − 0.32 to 0.22). For GER severity, eight QTLs were detected in KE jointly explaining 34% of the genetic variance. In PE, no significant QTLs for GER severity were detected. No common QTLs were found between GER severity and the three agronomic traits. The mean prediction accuracies ( $$\rho $$ρ ) of weighted GS (wRR-BLUP) were higher than $$\rho $$ρ of marker-assisted selection (MAS) and unweighted GS (RR-BLUP) for GER severity. Using KE as the training set and PE as the validation set resulted in very low $$\rho $$ρ that could be improved by using fixed marker effects in the GS model.

Rye is a multi‐purpose cereal crop grown in Central and Eastern Europe as well as in Western Canada. Fusarium head blight (FHB) is one of the diseases that have a severe negative impact on rye, but knowledge about FHB resistance at the genomic level is totally missing in rye. The objective of this study was to elucidate the genetic architecture of FHB resistance in winter rye using genome‐wide association (GWA) mapping complemented by genomic prediction (GP) in comparison with marker‐assisted selection (MAS). Additionally, plant height and heading stage were analysed. A panel of 465 S₁‐inbred lines of winter rye was phenotyped in three environments (location–year combinations) for FHB resistance by inoculation with Fusarium culmorum and genotyped with a 15k SNP array. Significant genotypic variation and high heritabilities were found for FHB resistance, heading stage and plant height. FHB did not correlate with heading stage, but was moderately correlated with plant height (r = −.52, p < .001) caused by some susceptible short inbred lines. The GWA scan identified 15 QTL for FHB resistance that jointly explained 74% of the genotypic variance. In addition, we detected 11 QTL for heading stage and 8 QTL for plant height, explaining 26% and 14% of the genotypic variance, respectively. A genome‐wide prediction approach resulted in 44% higher prediction abilities than marker‐assisted selection for FHB resistance. In conclusion, genomic approaches appear promising to improve and accelerate breeding for complex traits in winter rye.

Maize production is on risk by Gibberella ear rot (GER) caused byFusarium graminearum. This is one of the most important ear rot diseases in temperate zones as it leads to yield losses and production of harmful mycotoxins. We investigated, for the first time, the potential use of Brazilian tropical maize to increase resistance levels to GER in temperate European flint germplasm by analyzing six interconnected biparental populations. We assessed GER symptoms in Brazil and in Europe in up to six environments (= location × year combinations) during the growing seasons of 2018 and 2019. We conducted multi-parent QTL and biparental QTL mapping, and identified four QTLs with additive gene action, each explaining 5.4 to 21.8% of the total genotypic variance for GER resistance. Among them, QTL q1 was stable across test environments, populations, and between inbred lines and testcrosses. The accuracies of genomic prediction ranged from 0.50 to 0.59 depending on the resistance donor and prediction model. Jointly, our study reveals the potential use of Brazilian resistance sources to increase GER resistance levels by genomics-assisted breeding.

Predicting the resistance of hybrids from lines is a relevant approach for accelerating the improvement of disease resistance in hybrid breeding. In this study, genetic variation and covariation among 76 DH lines from two flint landraces, Kemater (KE) and Petkuser (PE), and their corresponding testcrosses (TC) were estimated for the first time for this material for Gibberella ear rot (GER), days to silking (DS), and plant height (PHT). Lines and TC were evaluated in four and two environments, respectively, under artificial infection with GER. TC were, on average, 42% less GER infected than their lines. TC matured 3–4 days earlier and were about 110 cm taller than the lines. GER resistance was 10% higher in KE lines and TC than PE lines and TC. Significant (p < 0.001) genotypic and genotype-by-environment interaction variances were found for all traits. Genotypic variances were generally smaller among TC than lines. Broad-sense heritability estimates were moderate to high for GER severity (0.56–0.82) and high for DS (0.78–0.88) and PHT (0.86–0.94) with higher values always observed in lines. Significant, moderate correlations between TC and line per se performance were found for GER resistance in both KE and PE (r = 0.37 and 0.55, respectively). For the two agronomic traits, correlations were higher (r = 0.59–0.76) than for GER resistance. Genomic prediction accuracies were moderate to high for GER resistance (r = 0.49–0.63) and generally higher for DS and PHT. In conclusion, a pre-selection of DH lines for GER resistance should be feasible; however, TC should be additionally tested on a later selection stage to aim for GER-resistant hybrid cultivars.