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

Abstract

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.

Global warming and increasing maize cultivation demand comprehensive efforts in disease and insect resistance breeding in north‐western Europe

“…Ideally, multiple‐disease and multiple‐insect resistance maize cultivars should be bred, although this is a challenging task (Kim et al, 2021), particularly when relying on traditional breeding methods only. These are supplemented today with off‐season nurseries, doubled‐haploid techniques, MAS, and GS procedures to reduce cycle length and enhance breeding population sizes (Miedaner et al, 2020; Sánchez‐Martín & Keller, 2019).…”

“…Similar to other pathosystems, a great array of resistance QTLs exists. In a recent study, 197 QTLs from 27 references were localized on all 10 chromosomes of maize (Miedaner et al, 2020). Again, the QTLs were not randomly distributed, but occurred in hotspots.…”

Climate change will influence disease resistance breeding in wheat in Northwestern Europe

“…About 75% of the cultivars included in the Descriptive List of Varieties (BSA 2020 ) are resistant to yellow rust with a score ranging from 1 to 3. Information on the genetic basis of these resistances is not available; however, an association study considering about 150 German winter wheat cultivars indicated a quantitative inheritance with 13 QTLs detected across three locations, each explaining 1.3–10.8% of the genotypic variance in the adult-plant stage (Miedaner et al 2020a ). The allelic effects of the main QTLs showed that 71–87% of the winter wheat lines already carried the resistance alleles.…”

“…Similarly, several QTL have been described in wheat that confer multiple resistances to a combination of two of the diseases STB, SNB, and FHB (Miedaner et al 2012 ). In a more recent approach, nine MDR QTL have been detected in a wheat diversity panel for resistances to four diseases, powdery mildew, yellow rust, stem rust, and FHB that have not been shown up in the individual disease resistances (Miedaner et al 2020a ). Combining such MDR QTL by applying marker-assisted or genomic selection seems a promising approach and should allow to react faster to changing pathogen populations or changes in the importance of diseases.…”

“…Although crop disease problems will not generally increase till the end of this century (Juroszek and von Tiedemann 2015 ) crop productivity must be especially safe-guarded by increasing the input into the breeding goal ‘yield stability’ (Miedaner 2018 ). Breeding for resistance, preferably multi-disease or broad-spectrum resistance (Li et al 2020 ; Miedaner et al 2020a ), against already existing and emerging diseases is an important component among others (e.g., water use efficiency, nitrogen use efficiency, low risk of lodging) to achieve yield stability (Chapman et al 2012 ). Therefore, plant breeding must address both abiotic (e.g., heat, drought, waterlogging, salinity) and biotic stresses (Ceccarelli et al 2010 ) including, for example, insect pests and pathogens, such as bacteria, phytoplasmas, viruses, fungi, oomycetes, and nematodes.…”