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

Key message High genetic variation in two European maize landraces can be harnessed to improve Gibberella ear rot resistance by integrated genomic tools. Abstract 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 ($${r}_{g}$$ r g ) correlations between GER severity and three agronomic traits were low (r = − 0.27 to 0.20; $${r}_{g}\hspace{0.17em}$$ r g = − 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.

Intercontinental trials reveal stable QTL for Northern corn leaf blight resistance in Europe and in Brazil

Key message NCLB is the most devastating leaf disease in European maize, and the introduction of Brazilian resistance donors can efficiently increase the resistance levels of European maize germplasm. Abstract Northern corn leaf blight (NCLB) is one of the most devastating leaf pathogens in maize (Zea mays L.). Maize cultivars need to be equipped with broad and stable NCLB resistance to cope with production intensification and climate change. Brazilian germplasm is a great source to increase low NCLB resistance levels in European materials, but little is known about their effect in European environments. To investigate the usefulness of Brazilian germplasm as NCLB resistance donors, we conducted multi-parent QTL mapping, evaluated the potential of marker-assisted selection as well as genome-wide selection of 742 F1-derived DH lines. The line per se performance was evaluated in one location in Brazil and six location-by-year combinations (= environments) in Europe, while testcrosses were assessed in two locations in Brazil and further 10 environments in Europe. Jointly, we identified 17 QTL for NCLB resistance explaining 3.57–30.98% of the genotypic variance each. Two of these QTL were detected in both Brazilian and European environments indicating the stability of these QTL in contrasting ecosystems. We observed moderate to high genomic prediction accuracies between 0.58 and 0.83 depending on population and continent. Collectively, our study illustrates the potential use of tropical resistance sources to increase NCLB resistance level in applied European maize breeding programs.

European maize genomes unveil pan-genomic dynamics of repeats and genes

The exceptional diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report high quality de novo genome sequences of the four European flint lines EP1, F7, DK105 and PE0075 assembled to pseudomolecules with scaffold N50 ranging between 6.1 to 10.4 Mb. Comparative analyses with the two US Corn Belt genomes B73 and PH207 elucidates the pronounced differences between both germplasm groups. While overall syntenic order and consolidated gene annotations reveal only moderate pan-genomic differences, whole genome alignments delineating the core and dispensable genome, and the analysis of repeat structures, heterochromatic knobs and orthologous long terminal repeat retrotransposons (LTRs) unveil the extreme dynamics of the maize genome. Haplotypes derived from core genome SNPs demonstrate the tessellation of modern maize resulting from a complex breeding history. The high quality genome sequences of the flint pool are a crucial complement to the maize pan-genome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.

Maize yields over Europe may increase in spite of climate change, with an appropriate use of the genetic variability of flowering time

Projections based on invariant genotypes and agronomic practices indicate that climate change will largely decrease crop yields. The comparatively few studies considering farmers’ adaptation result in a diversity of impacts depending on their assumptions. We combined experiments and process-based modeling for analyzing the consequences of climate change on European maize yields if farmers made the best use of the current genetic variability of cycle duration, based on practices they currently use. We first showed that the genetic variability of maize flowering time is sufficient for identifying a cycle duration that maximizes yield in a range of European climatic conditions. This was observed in six field experiments with a panel of 121 accessions and extended to 59 European sites over 36 years with a crop model. The assumption that farmers use optimal cycle duration and sowing date was supported by comparison with historical data. Simulations were then carried out for 2050 with 3 million combinations of crop cycle durations, climate scenarios, management practices, and modeling hypotheses. Simulated grain production over Europe in 2050 was stable (−1 to +1%) compared with the 1975–2010 baseline period under the hypotheses of unchanged cycle duration, whereas it was increased (+4–7%) when crop cycle duration and sowing dates were optimized in each local environment. The combined effects of climate change and farmer adaptation reduced the yield gradient between south and north of Europe and increased European maize production if farmers continued to make the best use of the genetic variability of crop cycle duration.

HaploBlocker: Creation of subgroup specific haplotype blocks and libraries

ABSTRACTThe concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach (“HaploBlocker”) for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium. We define a haplotype block as a sequence of genetic markers that has a predefined minimum frequency in the population and only haplotypes with a similar sequence of markers are considered to carry that block, effectively screening a dataset for group-wise identity-by-descent. From these haplotype blocks we construct a haplotype library that represents a large proportion of genetic variability with a limited number of blocks. Our method is implemented in the associated R-package HaploBlocker and provides flexibility to not only optimize the structure of the obtained haplotype library for subsequent analyses, but is also able to handle datasets of different marker density and genetic diversity. By using haplotype blocks instead of SNPs, local epistatic interactions can be naturally modelled and the reduced number of parameters enables a wide variety of new methods for further genomic analyses such as genomic prediction and the detection of selection signatures. We illustrate our methodology with a dataset comprising 501 doubled haploid lines in a European maize landrace genotyped at 501’124 SNPs. With the suggested approach, we identified 2’991 haplotype blocks with an average length of 2’685 SNPs that together represent 94% of the dataset.

Assessment of the influence of fertilisation and environmental conditions on maize health

Field experiments showed the occurrence of such agrophages as the frit fly (Oscinella frit L.) and the European maize borer (Pyrausta nubilalis Hbn.). Identified diseases included fusariosis (Fusarium ssp.) and maize smut (Ustilago maydis Corda). The incidence of the frit fly was influenced by weather conditions, mainly temperature, in the period from sowing to the BBCH 15–16 phase. Moderate temperature conditions contributed to the occurrence of the pest. The significantly highest percentage of plants damaged by larvae of this pest was recorded on maize fertilised only with potassium (K) and phosphorus with potassium (PK). In turn, the lowest percentage of plants damaged by frit fly larvae was recorded for maize fertilised with nitrogen and potassium (NK). The percentage of plants damaged by the European maize borer was influenced by temperature and humidity conditions in individual years of the study. The highest percentage of plants damaged by larvae of the pest was found in the vegetation season characterised by the highest amount of rainfall with the lowest mean daily air temperature. The presence of potassium in a given fertiliser combination, the application of manure or combined application of manure and mineral fertilisation resulted in an enhanced resistance of maize plants to Fusarium ssp. fungi. The significantly greatest infestation of maize plants by the fungus Ustilago maydis Corda was recorded in the treatment in which only nitrogen was applied. In turn, the lowest percentage of plants with symptoms of this disease was recorded in the treatment with the application of potassium alone and in the application of potassium together with phosphorus.