Exploiting genetic diversity in two European maize landraces for improving Gibberella ear rot resistance using genomic tools

Genome-Wide Association Study and Prediction of Tassel Weight of Tropical Maize Germplasm in Multi-Parent Population

Tassel weight (TW) is a crucial agronomic trait that significantly affects pollen supply and grain yield development in maize breeding. To improve maize yield and develop new varieties, a comprehensive understanding of the genetic mechanisms underlying tassel weight is essential. In this study, tropical maize inbred lines, namely CML312, CML373, CML444, and YML46, were selected as female parents and crossed with the elite maize inbred line Ye107, which served as the common male parent, to develop a multi-parent population comprising four F8 recombinant inbred line (RIL) subpopulations. Using 6616 high-quality single nucleotide polymorphism (SNP) markers, we conducted genome-wide association analysis (GWAS) and genomic selection (GS) on 642 F8 RILs in four subpopulations across three different environments. Through GWAS, we identified 16 SNPs that were significantly associated with TW, encompassing two stable loci expressed across multiple environments. Furthermore, within the candidate regions of these SNPs, we discovered four novel candidate genes related to TW, namely Zm00001d044362, Zm00001d011048, Zm00001d011049, and Zm00001d031173 distributed on chromosomes 1, 3, and 8, which have not been previously reported. These genes are involved in processes such as signal transduction, growth and development, protein splicing, and pollen development, all of which play crucial roles in inflorescence meristem development, directly affecting TW. The co-localized SNP, S8_137379725, on chromosome 8 was situated within a 16.569 kb long terminal repeat retrotransposon (LTR-RT), located 22.819 kb upstream and 26.428 kb downstream of the candidate genes (Zm00001d011048 and Zm00001d011049). When comparing three distinct GS models, the BayesB model demonstrated the highest accuracy in predicting TW. This study establishes the theoretical foundation for future research into the genetic mechanisms underlying maize TW and the efficient breeding of high-yielding varieties with desired tassel weight through GS.

Food Safety Aspects of Breeding Maize to Multi-Resistance against the Major (Fusarium graminearum, F. verticillioides, Aspergillus flavus) and Minor Toxigenic Fungi (Fusarium spp.) as Well as to Toxin Accumulation, Trends, and Solutions-A Review

Maize is the crop which is most commonly exposed to toxigenic fungi that produce many toxins that are harmful to humans and animals alike. Preharvest grain yield loss, preharvest toxin contamination (at harvest), and storage loss are estimated to be between 220 and 265 million metric tons. In the past ten years, the preharvest mycotoxin damage was stable or increased mainly in aflatoxin and fumonisins. The presence of multiple toxins is characteristic. The few breeding programs concentrate on one of the three main toxigenic fungi. About 90% of the experiments except AFB1 rarely test toxin contamination. As disease resistance and resistance to toxin contamination often differ in regard to F. graminearum, F. verticillioides, and A. flavus and their toxins, it is not possible to make a food safety evaluation according to symptom severity alone. The inheritance of the resistance is polygenic, often mixed with epistatic and additive effects, but only a minor part of their phenotypic variation can be explained. All tests are made by a single inoculum (pure isolate or mixture). Genotype ranking differs between isolates and according to aggressiveness level; therefore, the reliability of such resistance data is often problematic. Silk channel inoculation often causes lower ear rot severity than we find in kernel resistance tests. These explain the slow progress and raise skepticism towards resistance breeding. On the other hand, during genetic research, several effective putative resistance genes were identified, and some overlapped with known QTLs. QTLs were identified as securing specific or general resistance to different toxicogenic species. Hybrids were identified with good disease and toxin resistance to the three toxigenic species. Resistance and toxin differences were often tenfold or higher, allowing for the introduction of the resistance and resistance to toxin accumulation tests in the variety testing and the evaluation of the food safety risks of the hybrids within 2-3 years. Beyond this, resistance breeding programs and genetic investigations (QTL-analyses, GWAM tests, etc.) can be improved. All other research may use it with success, where artificial inoculation is necessary. The multi-toxin data reveal more toxins than we can treat now. Their control is not solved. As limits for nonregulated toxins can be introduced, or the existing regulations can be made to be stricter, the research should start. We should mention that a higher resistance to F. verticillioides and A. flavus can be very useful to balance the detrimental effect of hotter and dryer seasons on aflatoxin and fumonisin contamination. This is a new aspect to secure food and feed safety under otherwise damaging climatic conditions. The more resistant hybrids are to the three main agents, the more likely we are to reduce the toxin losses mentioned by about 50% or higher.

Effectiveness of introgression of resistance loci for Gibberella ear rot from two European flint landraces into adapted elite maize (Zea mays L.)

European flint landraces are a major class of maize possessing favorable alleles for improving host resistance to Gibberella ear rot (GER) disease which reduces yield and contaminates the grains with mycotoxins. However, the incorporation of these landraces into breeding programs requires a clear understanding of the effectiveness of their introgression into elite materials. We evaluated 15 pre-selected doubled haploid (DH) lines from two European flint landraces, "Kemater Landmais Gelb" (KE) and "Petkuser Ferdinand Rot" (PE), together with two adapted elite flint lines and seven standard lines for GER severity as the main trait, and several adaptation traits (plant height, days to silking, seed-set, plant vigor) across four environments. From this evaluation, three KE DH lines and one PE DH line, with the lowest GER severity, were selected and used as donor parents that were crossed with the two adapted and GER susceptible flint lines (Flint1 and Flint2) to develop six bi-parental DH populations with 34-145 DH lines each. Each DH population was evaluated across two locations. Correlations between GER severity, which was the target trait, and adaptation traits were weak (-0.02 to 0.19). GER severity of lines from PE landrace was on average 2-fold higher than lines from KE landrace, indicating a clear superiority of the KE landrace lines. Mean GER severity of the DH populations was 39.4-61.0% lower than the adapted elite flint lines. All KE-derived DH populations were on average more resistant (27.0-36.7%) than the PE-derived population (51.0%). Highly resistant lines (1.3-5.2%) were found in all of the populations, suggesting that the DH populations can be successfully integrated into elite breeding programs. The findings demonstrate that selected KE landrace lines used as donors were effective in improving GER resistance of the adapted elite inbreds.

Exploring GWAS and genomic prediction to improve Septoria tritici blotch resistance in wheat

Septoria tritici blotch (STB) is a destructive foliar diseases threatening wheat grain yield. Wheat breeding for STB disease resistance has been identified as the most sustainable and environment-friendly approach. In this work, a panel of 316 winter wheat breeding lines from a commercial breeding program were evaluated for STB resistance at the seedling stage under controlled conditions followed by genome-wide association study (GWAS) and genomic prediction (GP). The study revealed a significant genotypic variation for STB seedling resistance, while disease severity scores exhibited a normal frequency distribution. Moreover, we calculated a broad-sense heritability of 0.62 for the trait. Nine single- and multi-locus GWAS models identified 24 marker-trait associations grouped into 20 quantitative trait loci (QTLs) for STB seedling-stage resistance. The seven QTLs located on chromosomes 1B, 2A, 2B, 5B (two), 7A, and 7D are reported for the first time and could potentially be novel. The GP cross-validation analysis in the RR-BLUP model estimated the genomic-estimated breeding values (GEBVs) of STB resistance with a prediction accuracy of 0.49. Meanwhile, the GWAS assisted wRR-BLUP model improved the accuracy to 0.58. The identified QTLs can be used for marker-assisted backcrossing against STB in winter wheat. Moreover, the higher prediction accuracy recorded from the GWAS-assisted GP analysis implies its power to successfully select superior candidate lines based on their GEBVs for STB resistance.

Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat

Linkage disequilibrium (LD)-based haplotyping with subsequent SNP tagging improved the genomic prediction accuracy up to 0.07 and 0.092 for Fusarium head blight resistance and spike width, respectively, across six different models. Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r² < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Fusarium (FER) and Gibberella ear rots (GER) are the two most devastating diseases of maize (Zea mays L.) which reduce yield and affect grain quality worldwide, especially by contamination with mycotoxins. Genetic improvement of host resistance to effectively tackle FER and GER diseases requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. We applied improved meta-analysis algorithms to re-analyze 224 QTL identified in 15 studies based on dense genome-wide single nucleotide polymorphisms (SNP) in order to identify meta-QTL (MQTL) and colocalized genomic loci for fumonisin (FUM) and deoxynivalenol (DON) accumulation, silk (SR) and kernel (KR) resistances of both FER and GER, kernel dry-down rate (KDD) and husk coverage (HC). A high-resolution genetic consensus map with 36,243 loci was constructed and enabled the projection of 164 of the 224 collected QTL. Candidate genes (CG) mining was performed within the most refined MQTL, and identified CG were cross-validated using publicly available transcriptomic data of maize under Fusarium graminearum infection. The meta-analysis revealed 40 MQTL, of which 29 were associated each with 2-5 FER- and/or GER-related traits. Twenty-eight of the 40 MQTL were common to both FER and GER resistances and 19 MQTL were common to silk and kernel resistances. Fourteen most refined MQTL on chromosomes 1, 2, 3, 4, 7 and 9 harbored a total of 2,272 CG. Cross-validation identified 59 of these CG as responsive to FER and/or GER diseases. MQTL ZmMQTL2.2, ZmMQTL9.2 and ZmMQTL9.4 harbored promising resistance genes, of which GRMZM2G011151 and GRMZM2G093092 were specific to the resistant line for both diseases and encoded "terpene synthase21 (tps21)" and "flavonoid O-methyltransferase2 (fomt2)", respectively. Our findings revealed stable refined MQTL harboring promising candidate genes for use in breeding programs for improving FER and GER resistances with reduced mycotoxin accumulation. These candidate genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted backcross breeding strategies.

Novel Insights into the Inheritance of Gibberella Ear Rot (GER), Deoxynivalenol (DON) Accumulation, and DON Production

Gibberella ear rot (GER) is an important fungal ear pathogen of maize that causes ear rot and toxin contamination. Most previous works have only dealt with the visual symptoms, but not with the toxins of GER. As food and feed safety rankings depend on toxin contamination, including deoxynivalenol (DON), without toxins, nothing can be said about the risks involved in food and feed quality. Therefore, three susceptible, three medium-susceptible, and three medium-resistant mother lines were crossed with three testers with differing degrees of resistance and tested between 2017–2020. Two plot replicates and two fungal strains were used separately. The highest heterosis was found at the GER% with a 13% increase across 27 hybrids, including 7 hybrids showing negative heterosis (a higher hybrid performance above the parental mean), with a variance ranging between 63.5 and −55.4. For DON, the mean heterosis was negative at −35%, and only 10 of the 27 hybrids showed a positive heterosis. The mean heterosis for DON contamination, at 1% GER, was again negative (−19.6%, varying between 85% and 224%). Only 17 hybrids showed heterosis, while that of the other 17 was rated higher than the parental mean. A positive significant correlation was found only for GER% and DON; the other factors were not significant. Seven hybrids were identified with positive (2) or negative (5) heterosis for all traits, while the rest varied. For DON and GER, only 13 provided identical (positive or negative) heteroses. The majority of the hybrids appeared to diverge in the regulation of the three traits. The stability of GER and DON (variance across eight data sets) did not agree—only half of the genotypes responded similarly for the two traits. The genetic background for this trait is unknown, and there was no general agreement between traits. Thus, without toxin analyses, the evaluation of food safety is not possible. The variety in degrees of resistance to toxigenic fungi and resistance to toxin accumulation is an inevitable factor.

Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics

The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio^® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.

Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools

Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.

Importance of Landraces in Cereal Breeding for Stress Tolerance

The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.

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.

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 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.