Breeding for resistance to Fusarium ear diseases in maize and small-grain cereals using genomic tools

The worlds human and livestock population is increasing and there is the need to increase quality food production to achieve the global sustainable development goal 3, zero hunger by year 2030 (United Nations, 2015). However, biotic stresses such as Fusarium ear infections pose serious threat to cereal crop production. Breeding for host plant resistance against toxigenic Fusarium spp. is a sustainable way to produce more and safer cereal crops such as maize and small-grain winter cereals. Many efforts have been made to improve maize and small-grain cereals for ear rot (ER) and Fusarium head blight (FHB) resistances, using conventional and genomic techniques. Among small-grain cereals, rye had the shortest maturity period followed by the descendant, hexaploid triticale while both wheat species had the longest maturity period. In addition, rye and triticale were more robust to Fusarium infection and deoxynivalenol accumulation, making them safer grain sources for human and animal consumption. However, a few resistant cultivars have been produced by prolonged conventional breeding efforts in durum wheat and bread wheat. High genetic variation was present within each crop species and can be exploited for resistance breeding. In this thesis, the genetic architecture of FHB resistance in rye was investigated for the first time, by means of genome-wide association study (GWAS) and genomic prediction (GP). GWAS detected 15 QTLs for Fusarium culmorum head blight severity, of which two had major effects. Both weighted and unweighted GP approaches yielded higher prediction abilities than marker-assisted selection (MAS) for FHB severity, heading stage and plant height. Genomics-assisted breeding can shorten the duration of breeding rye for FHB resistance. In the past decade, genetic mapping and omics were used to identify a multitude of QTLs and candidate genes for ear rot resistances and mycotoxin accumulation in maize. The polygenic nature of resistance traits, high genotype x environment interaction, and large-scale phenotyping remain major bottlenecks to increasing genetic gains for ear rots resistance in maize. Phenotypic and molecular analyses of DH lines originating from two European flint landraces (Kemater Landmais Gelb, KE, and Petkuser Ferdinand Rot, PE) revealed high variation for Gibberella ear rot (GER) severity and three agronomic traits viz. number of days to female flowering, plant height and proportion of kernels per cob. By employing multi-SNP GWAS method, we found four medium-effect QTLs and many small-effect (10) QTLs for GER severity in combined DH libraries (when PCs used as fixed effects), none co-localized with the QTLs detected for the three agronomic traits analyzed. However, one major QTL was detected within KE DH library for GER severity. Two prioritized SNPs detected for GER resistance were associated with 25 protein-coding genes placed in various functional categories, which further enhances scientific knowledge on the molecular mechanisms of GER resistance. Genome-based approaches seems promising for tapping GER resistance alleles from European maize landraces for applied breeding. After several cycles of backcrossing and sufficient selection for agronomic adaptation traits, the resistant lines identified in this thesis can be incorporated into existing maize breeding programs to improve immunity against F. graminearum ear infection. Breeding progress can be faster using KE landrace than PE. A successful validation of QTLs identified in this thesis can pave way for MAS in rye and marker-assisted backcrossing in maize. Effective implementation of genomic selection requires proper design of the training and validation sets, which should include part of the current breeding population.Um das Ziel 3 für nachhaltige Entwicklung, das Ende des Hungers bis 2030 (United Nations, 2015) zu erreichen, muss durch den Anstieg der Weltbevölkerung die Nahrungsmittelproduktion deutlich erhöht werden. Gleichzeitig aber bedrohen Pflanzenkrankheiten wie Fusariosen die Getreideproduktion. Die Züchtung von Sorten mit Resistenzen gegen die (für Mensch und Tier) giftigen Pilze der Gattung Fusarium ist ein nachhaltiger Weg, um größere Mengen und weniger toxin-belastetes Getreide zu produzieren. Viele Versuche wurden unternommen, um die Resistenz gegen Kolbenfäule in Mais und gegen Ährenfusariosen (Fusarium head blight, FHB) in kleinkörnigem Getreide mit konventionellen und genomischen Züchtungsmethoden zu verbessern. In unseren Untersuchungen waren Roggen und Triticale am widerstandsfähigsten gegen Fusarium-Infektionen und hatten die geringste Deoxynivalenol-Kontamination, was sie zu weniger toxischen Nahrungs- und Futtermitteln macht. Aber auch für Hart- und Weichweizen gibt es durch langjährige konventionelle Züchtung einzelne resistente Sorten. Eine hohe genetische Variation konnte bei allen Getreidearten beobachtet werden und kann damit für zukünftige Resistenzzüchtung verwendet werden. In dieser Arbeit wurde zum ersten Mal mit Hilfe einer genomweiten Assoziationsstudie (genome-wide association study, GWAS) und genomischer Vorhersage (genomic prediction, GP) die genetische Architektur der Fusarium-Resistenz in Roggen untersucht. GWAS konnten 15 Loci (quantitative trait loci, QTL) für die Resistenz gegen Fusarium culmorum gefunden werden, zwei davon mit Haupt-Effekten (major effects). Sowohl die gewichtete als auch die ungewichtete genomische Vorhersage erzielten für Fusariumbefall, Ährenschieben und Wuchshöhe höhere Genauigkeiten als die markergestützte Selektion (marker-assisted selection, MAS). Genomische Daten können damit die Züchtung von Fusarium-resistentem Roggen beschleunigen. In den letzten zehn Jahren wurden genetische Kartierungen und Omics verwendet, um eine Vielzahl von QTLs und Kandidatengenen für Kolbenfäule-Resistenzen und Mykotoxin-Akkumulation in Mais zu identifizieren. Die komplexe Vererbung der Resistenzen, die hohen Genotyp x Umwelt-Wechselwirkungen und der Bedarf großer Versuche zur Phänotypisierung den genetischen Zuchtfortschritt für die Resistenz gegen Kolbenfäule bei Mais. Die phänotypische und genotypische Analyse von doppelt-haploiden Maislinien, die aus zwei europäischen Flint-Landrassen (Kemater Landmais Gelb, KE, and Petkuser Ferdinand Rot, PE) erstellt wurden, zeigte eine hohe genetische Variation für Kolbenfäule (Giberella ear rot, GER) und die drei weiteren agronomischen Merkmale Tage bis zur weiblichen Blüte, Wuchshöhe und Kornansatz. Durch Verwendung einer GWAS-Methode, die mehrere Markerloci gleichzeitig berücksichtigt (multi-SNP), konnten vier QTL mit mittleren Effekten und 10 QTL mit kleinen Effekten für die GER-Befallsstärke in kombinierten DH-Bibliotheken gefunden werden; keine davon war co-lokalisiert mit QTL für die drei analysierten agronomischen Merkmale. Innerhalb der KE DH-Bibliothek wurde jedoch ein Haupt-QTL für die GER-Befallsstärke festgestellt. Zwei ausgewählte SNP-Marker für die GER-Befallstärke waren mit 25 proteincodierenden Sequenzen assoziiert, die unterschiedlichen Funktionen zugeordnet werden konnten und damit das Wissen über die molekularen Mechanismen zur GER-Resistenz erweiterten. Eine genom-basierte Züchtungsmethode erscheint vielversprechend, um die GER-Resistenz in europäischen Mais-Landrassen für die angewandte Züchtung zu erschließen. Nach mehreren Zyklen von Rückkreuzung und Selektion auf agronomische Merkmale, können die resistenten Linien in einem bestehenden Mais-Zuchtprogramm verwendet werden, um die Resistenz gegen Kolbenfusariosen zu erhöhen. Der Zuchtfortschritt dürfte bei Verwendung der Landrasse KE höher sein als bei PE. Eine erfolgreiche Validierung der QTL, die in dieser Arbeit gefunden wurden, kann den Weg für eine markergestützte Selektion bei Roggen und Mais zur Erhöhung der Fusarium-Resistenz ebnen. Die effiziente Anwendung genomischer Selektionsmethoden bedarf der laufenden Erstellung von aktuellen Trainings- und Validierungssets, die jeweils einen Teil der aktuellen Zuchtpopulationen umfassen sollten

Genomics-assisted breeding for quantitative disease resistances in small-grain cereals and maize

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 su ering 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.Generar conocimiento impulsado por la genómica abre una manera de acelerar la reproducción de resistencias proceso por mapeo de familias o poblaciones y selección genómica. Los requisitos previos importantes son grandes poblaciones que se analizan genómicamente mediante matrices de marcadores de densidad media a alta y extensas fenotipado en ubicaciones y años de las mismas poblaciones. Esto último es importante para capacitar a un modelo genómico que se utiliza para predecir valores genómicos estimados de reproducción de fenotípicamente no probados genotipos. Después de revisar las características específicas de las resistencias cuantitativas y las características genómicas básicas técnicas, las posibilidades de reproducción asistida por genómica se evalúan para seis patosistemas con hongos hemi-biotróficos: cereales de grano pequeño / tizón de la cabeza por Fusarium (FHB), trigo / mancha de Septoria tritici (STB) y la mancha de Septoria nodorum (SNB), pudrición de la mazorca de maíz / Gibberella (GER) y pudrición de la mazorca por Fusarium (FER), maíz / tizón de la hoja del maíz del norte (NCLB). Por lo general, todas las resistencias cuantitativas a las enfermedades son causadas por cientos de QTL esparcidos por todo el genoma, pero a menudo disponibles en hotspots como se ejemplifica para Resistencia a NCLB en maíz. Debido a que todos los cultivos padecen muchas enfermedades, la resistencia a múltiples enfermedades (MDR) es un objetivo atractivo que puede seleccionarse mediante MDR QTL específico. Finalmente, la integración de datos genómicos en el proceso de mejoramiento para la introgresión de recursos genéticos y para la mejora.Estación Experimental Agropecuaria PergaminoFil: Miedaner, Thomas. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Galiano-Carneiro Boeven, Ana Luisa. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Galiano-Carneiro Boeven, Ana Luisa. Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA; AlemaniaFil: Sewodor Gaikpa, David. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Kistner, Maria Belén. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Kistner, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kistner, María Belén. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Grote, Cathérine Pauline. University of Hohenheim. State Plant Breeding Institute; Alemani

Multi-parent QTL mapping reveals stable QTL conferring resistance to Gibberella ear rot in maize

Maize production is on risk by Gibberella ear rot (GER) caused by Fusarium 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.EEA PergaminoFil: Galiano-Carneiro, Ana L. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Galiano-Carneiro, Ana L. Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA; AlemaniaFil: Kessel, Bettina. Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA; AlemaniaFil: Presterl, Thomas. Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA; AlemaniaFil: Gaikpa, David Sewordor. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Kistner, María Belén. University of Hohenheim. State Plant Breeding Institute; AlemaniaFil: Kistner, María Belén. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Departamento de Maíz; ArgentinaFil: Kistner, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Miedaner, Thomas. University of Hohenheim. State Plant Breeding Institute; Alemani

Characterizing Winter Wheat Germplasm for Fusarium Head Blight Resistance Under Accelerated Growth Conditions

Fusarium head blight (FHB) is one of the economically important diseases of wheat as it causes severe yield loss and reduces grain quality. In winter wheat, due to its vernalization requirement, it takes an exceptionally long time for plants to reach the heading stage, thereby prolonging the time it takes for characterizing germplasm for FHB resistance. Therefore, in this work, we developed a protocol to evaluate winter wheat germplasm for FHB resistance under accelerated growth conditions. The protocol reduces the time required for plants to begin heading while avoiding any visible symptoms of stress on plants. The protocol was tested on 432 genotypes obtained from a breeding program and a genebank. The mean area under disease progress curve for FHB was 225.13 in the breeding set and 195.53 in the genebank set, indicating that the germplasm from the genebank set had higher resistance to FHB. In total, 10 quantitative trait loci (QTL) for FHB severity were identified by association mapping. Of these, nine QTL were identified in the combined set comprising both genebank and breeding sets, while two QTL each were identified in the breeding set and genebank set, respectively, when analyzed separately. Some QTLs overlapped between the three datasets. The results reveal that the protocol for FHB evaluation integrating accelerated growth conditions is an efficient approach for FHB resistance breeding in winter wheat and can be even applied to spring wheat after minor modifications

Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53-0.75 and 0.36-0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines

Towards Sustainable Maize Production: Understanding the Morpho-Physiological, Genetics, and Molecular Mechanisms for Tolerance to Low Soil Nitrogen, Phosphorus, and Potassium

Maize is one of the globally most important cereal crops used for food, feed and fuel. It requires optimum soil nutrients such as Nitrogen (N), Phosphorus (P), and Potassium (K) for proper growth and development as well as for tolerance to biotic and other abiotic stresses. Yield potentials are not met under suboptimal soil fertility. One of the innovations that can reduce environmental impacts of continuous fertilization and lower the cost of maize production under low soil nutrient conditions is the development and use of tolerant cultivars. This paper provides spotlights on the following: (1) morphology and physiology of root and shoot systems; (2) genetics and genomics; and (3) transcriptome, proteome, and metabolome profiles, to elucidate maize tolerance to low amounts of soil nutrients, N, P, and K. Maize cultivars having deeper rooting structure, more lateral roots, dense roots, and high root exudates are more tolerant to N, P, and K limited conditions. Cultivars that are tolerant to N, P, and K stress (low) have high nutrient use efficiency, good photosynthetic and translocation activity that support high aboveground shoot weight under suboptimal N, P, and K conditions. Maize tolerance to N, P, and K stress (low) is quantitative, and mainly controlled by additive genes. Maize cultivar development and dissemination programs can exploit the mechanisms highlighted in this review

Towards Sustainable Maize Production: Understanding the Morpho-Physiological, Genetics, and Molecular Mechanisms for Tolerance to Low Soil Nitrogen, Phosphorus, and Potassium

Maize is one of the globally most important cereal crops used for food, feed and fuel. It requires optimum soil nutrients such as Nitrogen (N), Phosphorus (P), and Potassium (K) for proper growth and development as well as for tolerance to biotic and other abiotic stresses. Yield potentials are not met under suboptimal soil fertility. One of the innovations that can reduce environmental impacts of continuous fertilization and lower the cost of maize production under low soil nutrient conditions is the development and use of tolerant cultivars. This paper provides spotlights on the following: (1) morphology and physiology of root and shoot systems; (2) genetics and genomics; and (3) transcriptome, proteome, and metabolome profiles, to elucidate maize tolerance to low amounts of soil nutrients, N, P, and K. Maize cultivars having deeper rooting structure, more lateral roots, dense roots, and high root exudates are more tolerant to N, P, and K limited conditions. Cultivars that are tolerant to N, P, and K stress (low) have high nutrient use efficiency, good photosynthetic and translocation activity that support high aboveground shoot weight under suboptimal N, P, and K conditions. Maize tolerance to N, P, and K stress (low) is quantitative, and mainly controlled by additive genes. Maize cultivar development and dissemination programs can exploit the mechanisms highlighted in this review

Variance Components and Correlations between Doubled Haploid Lines from Two European Flint Landraces and Their Corresponding Testcrosses for Gibberella Ear Rot Resistance, Silking Time, and Plant Height in Maize

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