Browsing by Subject "Maize"

Now showing 1 - 20 of 57

Adaptations of maize to low phosphate availability : establishing regulatory networks from large-scale quantitative proteomic profiling
(2022) He, Mingjie; Schulze, Waltraud
Maize (Zea mays) is an important crop in global for human food, animal feed and industrial usage. Suboptimal phosphorus (P) availability is one of the primary constraints for maize growth and productivity (Jianbo Shen et al., 2011; L.pez-Arredondo et al., 2014). Over 70% arable land suffers from P-deficiency, and plants can take up small amounts of P from the soil due to P-fixation. However, over-application of P fertilizer has frequently happened in last decades and resulted in environmental pollution (L.pez- Arredondo et al., 2014). Modern agriculture calls for maintaining productivity while reducing synthetic-P fertilizer inputs and losses, thus, requiring breeding of novel cultivars to increase phosphate use efficiency (PUE) (Balemi and Negisho, 2012; X., Li, Mang, et al., 2021; Mardamootoo et al., 2021). Understanding the regulation of maize to low phosphate(LP)-availability at the molecular level will offer unlimited potential for the development of selection markers and engineering targets in breeding programs. Nowadays, “OMIC” approaches and computational science are developing rapidly. They are advanced tools for investigation of molecular adaptations on a large-scale and in a systemic view. Thereby, the major research task within this thesis is to reveal P-deficiency induced responsive components and regulations at protein level based on proteomic profiles, aiming to provide promising candidate genes/proteins for research on the molecular mechanisms of adaptation to LP-stress, and potentially to provide promising candidate gene/proteins for development of selection markers and engineering targets to obtain desired traits, in the long term goal of improving PUE in novel cultivars. In Chapter 1, we focused on six genotypes (EP1, F2, F142, F160, SF1, SM1) with close genetic background but several contrasting traits to LP-stress, such as PUE (X., Li, Mang, et al., 2021). They were cultured in pot with either sufficient or inefficient P-fertilizer in a climate chamber for one month. The young seedlings were sampled by root and shoot for analysis of multiple traits, transcriptome and proteome. Firstly, we constructed the co-expression network of proteins and transcripts separately using WGCNA method (Langfelder and Horvath, 2008), which predicted potential protein-protein interactions or their co-regulations. Secondly, we categorized proteins/transcripts to modules according to their different coexpression patterns, thus, identified potential determining relationships of modules-traits. Thirdly, we compared the responses between transcripts and proteins, presenting their responses being concordant or dis-concordant. Fourthly, we identified common and genotype-specific P-starvation response modules and biological processes. Finally, we focused on protein kinases, which play roles as regulators, to demonstrated protein kinases-centered network and validated protein interactions between mitogenactivated protein kinase-kinase 1 (MEK1, Zm00001d043609) either with sucrose synthase1 (SH1,Zm00001d045042) or translation elongation factor 1-gamma 3 (eEF1B-γ, Zm00001d046352). MEK1 is a potential genotype-specific regulator via sucrose metabolism and translation elongation process. In Chapter 2, we aimed to adapted an experimental workflow for phosphoproteome analysis in maize, addressing the interference to phosphoproteome quantification by fibers, secondary metabolites and low abundant of phosphorylated proteins. In this manuscript, we described a rapid and universal protocol for both proteome and phosphoproteome analysis that is suitable for cereal crops. The results of phosphoproteome in maize root testing samples showed that proteins within kinase-centered network in Chapter 1 can be largely quantified based on this workflow. It provides a possible way to analyze phosphorylation dynamics to P-starvation responses, it allows further investigation for kinase-centered 1 network in Chapter 1 to identify phosphorylation pairs of “protein kinase – protein substrate”, which will largely expand a view on P-starvation regulations through posttranslational modifications.
Application of Near-Infrared Spectroscopy in Plant Breeding Programs
(2006) Montes, Juan Manuel; Melchinger, Albrecht E.
The success of plant breeding programs depends on the availability of genetic variation and efficient data collection processes that allow large-scale screenings of genotypes. When genetic variation is present, the goal is to identify those genotypes that are closest to the breeding objectives. In this context, the evaluation of a large number of genotypes requires optimization of the data collection process in order to provide reliable information for making selection decisions. The process of data collection must yield an accurate and precise assessment of genotypes timely because the information is needed to plan the next generation for breeding and cultivar development. Laboratory NIRS is routinely used in the data collection process of many breeding programs, but it requires the withdrawal of field plot samples and involves manual work. Applications of the near-infrared spectroscopy on choppers (NOC) and near-infrared spectroscopy on combine harvester (NOCH) are a step forward to the automation of data collection processes, by which sampling, labor, and sources of error in the data can be reduced. The objective of this thesis research was to assess the potential of NOC and NOCH for application in breeding programs of grain maize, rapeseed, and silage maize. Plot combine harvesters and choppers were equipped with diode-array spectrometers for collection of near-infrared plot spectra, and used to harvest experimental varieties of breeding programs in Central Europe. Two alternative sample presentation designs (conveyor belt and spout) were used for the NOC systems. The NOCH systems used the conveyor belt as sample presentation design. NOCH showed a high potential for determination of dry matter (DM), crude protein (CP), and starch (ST) contents of maize grain. NOCH calibration models yielded standard errors of prediction (SEP) and coefficients of determination of validation (R2V) of 1.2% and 0.95 for DM, 0.3% and 0.88 for CP, and 1.0% and 0.79 for ST, respectively. The potential of NOCH for determination of DM, CP, oil and glucosinolate contents of rapeseed was also high. NOCH calibration models yielded standard errors of cross validation (SECV) and coefficients of determination of cross validation (R2CV) of 0.3% and 0.96 for DM, 0.6% and 0.69 for CP, 0.9% and 0.71 for oil, and 2.2 μmol/g and 0.40 for glucosinolate, respectively. The NOC systems showed high potential for the determination of DM, ST, and soluble sugars (SS) content of silage maize hybrids. The NOC system equipped with a conveyor belt design yielded calibration models with SEP and R2V of 0.9% and 0.93 for DM, and 2.1% and 0.78 for ST, respectively. For the NOC system equipped with the spout design, the SEP and R2V amounted to 1.4% and 0.84 for DM, 2.3% and 0.75 for ST, and 0.9% and 0.81 for SS. The potential of both NOC systems for determination of fiber contents (CF, ADF, and NDF), digestibility and energy-related traits was lower than for DM, ST, and SS. The precision of NOCH for the determination of DM content in maize grain was higher than by traditional drying-oven method. A higher precision of NOCH is also expected for other traits and may also be extended to the NOC systems because the sampling error associated with traditional processes of data collection is reduced drastically by NOC and NOCH. The investigation of the effects caused by the calibration technique, mathematical transformation of the near-infrared spectra, and scatter correction on the development of NOCH calibration models for the prediction of DM, CP, and ST content in maize grain revealed that calibration technique was the most important factor affecting the prediction ability, whereas the importance of mathematical transformation and scatter correction depended on the particular constituent considered. Presently, there exists high uncertainty about the optimal NOC and NOCH sample presentation designs for agricultural harvesters. The dynamic signal range, i.e., the range of spectral values on which predictions are based, and the amount of plot material measured were identified as guide parameters for optimization of sample presentation designs. In addition, calibration transferability between NOC systems with different sample presentation designs proved to be feasible after merging spectra from both NOC systems in the calibration set. In conclusion, NOC and NOCH show high potential for replacing laboratory NIRS analysis of several traits in a plant breeding context and yield a more accurate and precise evaluation of field plot characteristics. Therefore, technological applications of the electromagnetic radiation is predicted to have a high impact in plant breeding, precision farming, and agriculture.
Assessing the genetic variation of phosphate efficiency in European maize (Zea mays L.)
(2022) Weiß, Thea Mi; Würschum, Tobias
Why should plant breeders in Central Europe care about phosphate efficiency? Soil phosphorus levels have mostly reached high to very high levels over the last decades in intensively farmed, livestock-rich regions. However, the European Union demands a restructuring of the agricultural production systems through setting ambitious goals envisaged in the Farm to Fork Strategy. By 2030, fertilizer use should be reduced by 20 %, nutrient losses by at least 50 %. As a consequence, farmers have to be even more efficient with crop inputs, among them the globally limited resource of phosphorus fertilizers, while maintaining high yields. Plant breeding means thinking ahead. Therefore, phosphate-efficient varieties should be developed to help farmers meet this challenge and reduce the need for additional fertilizers. One prerequisite to reach this target is that genotypic variation for the relevant traits is available. Moreover, approaches that assist selection by accurate but also time- and resource-efficient prediction of genotypes are highly valuable in breeding. Finally, the choice of the selection environment and suitable trait assessment for the improvement of phosphate efficiency under well-supplied conditions, need to be elaborated. In this dissertation, a diverse set of maize genotypes from ancient landraces to modern hybrids was investigated for phosphate efficiency-related traits under well-supplied P soil conditions. Multi-environmental field trials were conducted in 2019 and 2020. The reaction to different starter fertilizer treatments of the 20 commercially most important maize hybrids grown in Germany was studied. In the hybrid trial, the factor environment had a significant effect on the impact of starter fertilizers. Especially in early developmental stages genotypes showed a different response to the application of starter fertilizers. On the overall very well-supplied soils, we observed no significant genotype-by-starter fertilizer interaction. Nonetheless, we identified hybrids, which maintained high yields also if no starter fertilizer was provided. Thus, it seems that sufficient variation is available to select and breed for phosphate efficiency under reduced fertilizer conditions. Furthermore, the concept of phenomic prediction, based on near-infrared spectra instead of marker data to predict the performance of genotypes, was applied to 400 diverse lines of maize and compared to genomic prediction. For this, we used seed-based near-infrared spectroscopy data to perform phenomic selection in our line material, which comprised doubled haploid lines from landraces and elite lines. We observed that phenomic prediction generally performed comparable to genomic prediction or even better. In particular, the phenomic selection approach holds great potential for predictions among different groups of breeding material as it is less prone to artifacts resulting from population structure. Phenomic selection is therefore deemed a useful and cost-efficient tool to predict complex traits, including phosphorus concentration and grain yield, which together form the basis to determine phosphate efficiency. Lastly, 20 different indicators for phosphate efficiency were calculated, the genetic variation of the different measures present in this unique set of lines was quantified, and recommendations for breeding were derived. Of the different measures for phosphate efficiency reported in literature, Flint landraces demonstrated valuable allelic diversity with regard to phosphate efficiency during the seedling stage. Due to the highly complex genetic architecture of phosphate efficiency-related traits, a combination of genomic and phenotypic selection appears best suited for their improvement in breeding. Taken together, phosphate efficiency, including its definition and meaning, is largely dependent on the available phosphorus in the target environment as well as the farm type, which specifies the harvested produce and thereby the entire phosphorus removal from the field. In conclusion, future maize breeding should work in environments that are similar to the future target environments, meaning reduced fertilizer inputs and eventually lower soil P levels. Our results demonstrate that breeding of varieties, which perform well without starter fertilizers is feasible and meaningful under the well-supplied conditions prevalent in Central Europe. For the improvement of the highly complex trait phosphate efficiency through breeding we recommend to apply genomic and phenomic prediction along with classical phenotypic screening of genotypes and by this making our food systems more resilient towards upcoming challenges in agriculture.
Biometrical Analyses of Epistasis and the Relationship between Line per se and Testcross Performance of Agronomic Traits in Elite Populations of European Maize (Zea mays L.)
(2005) Mihaljevic, Renata; Melchinger, Albrecht E.
Relations of yield and other important agronomic traits of inbred lines to the same traits in hybrids have been studied from the time of initiation of hybrid breeding to the present. Because crossing lines to a tester and conducting yield trials are expensive and time-consuming, reliable information on inbred lines that is indicative of their testcross performance is crucial for optimum testing schemes in hybrid breeding as well as simultaneous improvement of commercial hybrids and their inbred parents. It has therefore been of great importance to determine the magnitude of correlation between line per se performance (LP) and testcross performance (TP) and investigate if epistasis influences this correlation. The comprehensive study on hand was performed with five populations (F3 to F6 lines) differing in size (ranging from 71 to 344), level of inbreeding, and the number of common parents. The populations employed were derived from three biparental crosses within the heterotic pool of European elite flint maize (Zea mays L.). All five populations were evaluated for TP (using an unrelated dent tester inbred) of five agronomically important quantitative traits: grain yield, grain moisture, kernel weight, protein concentration, and plant height. Four of these populations were also evaluated for LP of the same five traits. The objectives were to (i) estimate phenotypic and genotypic correlations between LP and TP within four populations for all five traits, (ii) map quantitative trait loci (QTL) for LP and TP in four and five populations, respectively, for all five traits, (iii) validate estimated QTL effects and positions for TP by assessing QTL congruency among testcross populations differing in size and genetic background, (iv) determine the value of LP-QTL for the prediction of TP, (v) estimate the importance of epistatic effects for LP and TP of grain yield and grain moisture by generation means analysis as well as genome-wide testing for epistatic marker pairs, and (vi) draw conclusions regarding the prospects of marker-assisted selection (MAS). Genotypic correlations between LP and TP, rg(LP, TP), estimated herein were comparable with those obtained for European flint or U.S. dent material. The magnitude of rg(LP, TP) was trait-specific: for traits of high heritability, i.e. grain moisture, kernel weight, protein concentration, and plant height, estimates were generally larger than 0.7 across all four populations, whereas for grain yield, estimates were consistently lower and did not exceed the intermediate level of 0.5. For grain yield, lowest rg(LP, TP) were estimated with lowest precision (largest confidence intervals). This requires testing for both LP and TP and/or combining the data in a selection index to ensure sufficient inbred performance (seed production) and yield improvement. However, combined selection for LP and TP proved less efficient than sole selection for TP unless unadapted material was employed. For kernel weight, protein concentration, and plant height, we detected "large" congruent QTL across testcross populations derived from the same cross, which individually explained up to 46% of the validated genotypic variance p. However, as the p values estimated from validation were still below the corresponding heritability estimates, MAS will be superior to phenotypic selection only if it is more cost-efficient. For the above traits, similar numbers of QTL for LP and TP were detected across populations. More than half of the QTL regions detected for LP were in common for LP and TP in the largest population (N = 280). To assess the value of QTL identified for LP in predicting TP, we calculated the genotypic correlation rg(MLP, YTP). This parameter assesses QTL congruency for LP and TP quantitatively and is thus the key parameter for assessing the prospects of MAS. The number of common QTL for LP and TP (qualitative QTL congruency) was generally not indicative of the magnitude of rg(MLP, YTP) due to the differences in the effect size of the respective QTL detected for LP and used for the prediction of TP. For all traits, rg(MLP, YTP) were smaller than rg(LP, TP). This is because rg(MLP, YTP) is only predictive for the validated proportion of genotypic variance explained by the QTL for LP, which was generally below 50% because of the limited power of QTL detection, in particular with small sample sizes below 100. Only if QTL detected for LP explain a substantial proportion of the genotypic variance, MAS based on these QTL can be applied, provided it is more cost-efficient than an indirect phenotypic selection for TP based on LP. QTL detection power was drastically reduced for the complex trait grain yield with a presumably large number of small QTL underlying its genetic architecture. Thus, the number of common QTL for LP and TP as well as the QTL congruency across testcross populations was much lower for grain yield than the other four traits. Estimated gene action of QTL detected for LP was primarily additive for grain yield. Evidence for dominance and/or epistasis, which may be a reason for the low rg(LP, TP) and the low number of common QTL for LP and TP was generally weak. Both generation means analysis for LP and TP and genome-wide search for epistatic marker pairs yielded no evidence for epistasis. This is not only because the detected epistatic effects could not be validated, but also because there is low chance to find epistasis unless the generation examined displays the full epistatic variance such as expected from doubled haploids produced from an F1 cross. Thus, it is anticipated that the relative importance of epistatic effects in hybrid maize breeding may strongly increase with the currently happening shift in line development from recurrent selfing towards the production of doubled haploids.
Can we abandon phosphorus starter fertilizer in maize? Results from a diverse panel of elite and doubled haploid landrace lines of maize (Zea mays L.)
(2022) Roller, Sandra; Weiß, Thea M.; Li, Dongdong; Liu, Wenxin; Schipprack, Wolfgang; Melchinger, Albrecht E.; Hahn, Volker; Leiser, Willmar L.; Würschum, Tobias
The importance of phosphorus (P) in agriculture contrasts with the negative environmental impact and the limited resources worldwide. Reducing P fertilizer application by utilizing more efficient genotypes is a promising way to address these issues. To approach this, a large panel of maize (Zea mays L.) comprising each 100 Flint and Dent elite lines and 199 doubled haploid lines from six landraces was assessed in multi-environment field trials with and without the application of P starter fertilizer. The treatment comparison showed that omitting the starter fertilizer can significantly affect traits in early plant development but had no effect on grain yield. Young maize plants provided with additional P showed an increased biomass, faster growth and superior vigor, which, however, was only the case under environmental conditions considered stressful for maize cultivation. Importantly, though the genotype-by-treatment interaction variance was comparably small, there is genotypic variation for this response that can be utilized in breeding. The comparison of elite and doubled haploid landrace lines revealed a superior agronomic performance of elite material but also potentially valuable variation for early traits in the landrace doubled haploid lines. In conclusion, our results illustrate that breeding for P efficient maize cultivars is possible towards a reduction of P fertilizer in a more sustainable agriculture.
Design of breeding strategies for energy maize in Central Europe
(2012) Grieder, Christoph; Melchinger, Albrecht E.
The area of maize (Zea mays L.) grown for production of biogas has tremendously increased in Germany during the past decade. Thus, breeding companies have a keen interest to develop special varieties for this new market segment. A high methane yield per area (MY), which depends multiplicatively on dry matter yield (DMY) and methane fermentation yield (MFY), is required to ensure the efficiency of biogas maize cultivation. However, information on the targeted biogas maize ideotype is still missing and estimates of relevant quantitative genetic parameters for representative material are required to design optimum breeding strategies. We conducted a large field experiment to assess the relevant traits in biogas maize, their variation, and associations among them. In detail, our objectives were to (1) determine MFY and its production kinetics as well as the chemical composition, (2) examine the relationship of MFY and traits related to its kinetics with plant chemical composition and silage quality traits like in vitro digestible organic matter (IVDOM) and metabolizable energy concentration (MEC); (3) examine the potential of near infrared spectroscopy (NIRS) for prediction of traits related to methane production; (4) evaluate a large population of inbred lines and their testcrosses under field conditions for agronomic and quality traits; (5) estimate variance components and heritabilities (h2) of traits relevant to biogas production; (6) study correlations among traits as well as between inbred line per se (LP) and testcross performance (TP); and (7) draw conclusions for breeding maize as a substrate for biogas production. For this purpose, a representative set of 285 dent inbred lines from diverse origins and their 570 testcross progenies with two adapted flint testers was produced. Both material groups were evaluated in field experiments conducted in six environments (three locations, two years) in Germany. For analysis of MFY, samples of a diverse core set of 16 inbred lines and their 32 testcrosses were analyzed using the Hohenheim Biogas Yield Test, a discontinuous, laboratory fermentation assay. The kinetics of methane production was assessed by non-linear regression. Estimates of h2 for MFY measured after short fermentation time (3 days) were high, but genotypic variance and, therefore, also h2 decreased towards the end of the fermentation period (35 days). This was presumably the consequence of a nearly complete degradation of all chemical components during the long fermentation period. This interpretation was supported by strong correlations of MFY with chemical components, IVDOM and MEC for the early, but not the late fermentation stages. Based on the samples in the core set, NIRS calibrations were developed for MFY, parameters related to the kinetics of methane production, and chemical composition. With a coefficient of determination from validation (R2V) of 0.82, accuracy of prediction was sufficiently high for the maximum methane production rate, which is related to the early fermentation phase, but not satisfactory for the time needed to reach 95% of a sample?s final MFY (R2V = 0.51). In agreement with the trend of h2, performance of NIRS to predict MFY on day 35 (R2V = 0.77) was lower than for MFY on day 3 (R2V = 0.85), but still at a satisfactory level, as was the case for concentrations of different chemical components. Hence, NIRS proved to be a powerful tool for prediction of MFY and chemical composition in the main experiment. For TP, estimates of variance components from the main experiments revealed that general combining ability (GCA) was the major source of variation. The very tight correlation of MY with DMY but not with MFY indicated that variation in MY was primarily attributable to differences in DMY. Compared to MEC, MFY showed a weaker association with chemical composition. Genotypic correlation (rg) of MFY was strongest with non-degradable lignin (-0.58). Correlation of MFY with starch was not significant and indicated a lower importance of high cob proportions for biogas maize than for forage maize. Hence, to improve MY, selection should primarily focus on increasing DMY. Results for LP in the main experiment largely confirmed results from testcrosses and favor selection for high dry matter yielding genotypes with less emphasis on ear proportion. Estimates of rg between LP and GCA were highest (> 0.94) for maturity traits (days to silking, dry matter concentration) and moderate (> 0.65) for DMY and MY. Indirect selection for GCA on basis of LP looks promising for maturity traits, plant height, and to some extent also for DMY.
Development of a generic, model-based approach to optimize light distribution and productivity in strip-intercropping systems
(2014) Munz, Sebastian; Claupein, Wilhelm
Due to a growing world population, an extension of bioenergy production and the larger proportion of meat and dairy products in the human diet, with the latter particularly in India and China, the demand for agricultural products will further increase. Under decreasing resources and negative environmental impacts related to past intensification, more sustainable agricultural production systems need to be developed in order to meet the future demand for agricultural products. China, as the most populous nation with an enormous economic growth since the end of the 1970’s, plays a major role in global agricultural production. On a national level, agricultural production has to be increased by 35% during the next 20 years. However, land and water resources in China are very limited. With this in mind, the Sino-German International Research Training Group (IRTG) entitled ‘Modeling Material Flows and Production Systems for Sustainable Resource Use in Intensified Crop Production in the North China Plain’ was initiated by the Deutsche Forschungs-Gemeinschaft (DFG) and the Chinese Ministry of Education (MOE). The present doctoral thesis was embedded in the IRTG and focused, in particular, on exploring combinations of different crops produced on the same land at the same time, known as intercropping. In general, the higher productivity in intercropping, compared with monocropping, arises from the complementary use of resources (radiation, water, and nutrients) over space and time by crops that differ in physiology, morphology and phenology. The decisive question is how to optimize intercropping systems over space and time. To address this question, the present doctoral thesis combined field experiments with modeling approaches with the following aims: (i) to investigate the light availability on high temporal and spatial resolutions; (ii) to develop and validate a model that simulates the light availability for the smaller crop and accounts for the major aspects of cropping design; (iii) to determine the effect of the modified light availability on growth of maize and the smaller, shaded crop; (iv) to evaluate the plant growth model CROPGRO for its ability to simulate growth of the smaller, shaded crop; (v) to investigate the interactions between maize cultivar, cropping design and local growth conditions; and, (vi) to identify promising cropping designs and detect future research needs to increase the productivity of strip-intercropping systems. For this purpose, field experiments comprising of strip-intercropping with maize (Zea mays L.) and smaller vegetables, including bush bean (Phaseolus vulgaris L. var. nana), were carried out over three growing seasons from 2010-2012 in southwestern Germany and in the North China Plain. Growing the crops in strips facilitates mechanized management, addressing the ongoing decrease of intercropping in China due to labor scarcity in rural areas. The crop combination of maize, a tall C4-crop with erectophile leaves, and bush bean, a small, N-fixating C3-crop with a more horizontal leaf orientation, was chosen due to the large potential for a complementary resource use. Special emphasis was given on the competition for light as it plays a major role in this cropping system due to the large height differences between the crops. In this context, measurements of the photosynthetically active radiation (PAR) were conducted on high spatial (individual rows across the strip) and temporal resolutions (five-minute intervals) at the top of the bush bean canopy over a two-month co-growing period with maize. The collected data formed the basis of the simulation study towards investigating competition for light and its influence on plant growth with modeling approaches. Experimental results showed that maize yields increased in the border rows of the strip due to a higher lateral incoming radiation in years with a sufficient water supply. On average, maize yields calculated for strips consisting of 18 to four rows increased by 3 to 12% and 5 to 24% at the German and Chinese sites, respectively. Analysis of yield components revealed that yield increases in the border rows of the maize strip were mainly determined by a larger number of kernels per plant. On the other hand, shading by the taller adjacent maize induced considerable shade adaptations of bush bean, such as larger canopy dimensions and a substantially increased leaf area index due to thinner, larger leaves. These shade adaptations increased light interception, and indicated that bush bean could tolerate shading up to 30%, resulting in a total and pod dry matter similar to that of monocropped bush bean. These results suggested that there is a good potential for utilizing bush bean in strip-intercropping systems in combination with taller crops. However, higher shade levels (>40%) resulted in considerable decreases of total and pod dry matter. The high temporal and spatial resolution of the PAR measurements clearly revealed a highly heterogeneous diurnal distribution of PAR across the bush bean strip. The developed light model simulated this heterogeneity with a high accuracy under both clear and cloudy conditions. Comparison of simulated and observed hourly values of PAR across several rows within the strip of bush bean showed a root mean square error (RMSE) ranging between 47 and 87 μmol m-2 s-1 and a percent bias (PBIAS) ranging between -3.4 and 10.0%. Furthermore, the model reasonably captured the influence of different widths of the bush bean strip, strip orientations and maize canopy architecture (height, leaf area index, and leaf angle distributions). Simulations run for different latitudes and sky conditions, including different strips widths, maize canopy heights and leaf area indices (LAI), indicate that: (i) increasing the strip width might only reduce shading in the border rows of the smaller crop at lower latitudes under a high fraction of direct radiation; (ii) at higher latitudes, the selection of a maize cultivar with reduced height and LAI are suitable options to increase the light availability for the smaller crop. The present doctoral thesis presents the first approach to use the monocrop plant growth model CROPGRO to simulate growth of a legume crop grown in an intercropping system. The CROPGRO model was chosen because it provides an hourly simulation of leaf-level photosynthesis, and algorithms that account for the effects of radiation intensity on canopy dimensions and specific leaf area. CROPGRO, calibrated on data of monocropped bush bean, captured, quite well, the effects of the strongly reduced radiation on leaf area, and total and pod dry matter in the most shaded bush bean row. This indicated the models’ applicability on other intercropping systems exhibiting high levels of shading. Under a lower level of shading, cultivar and ecotype parameters had to be calibrated individually for a respective row within the bush bean strip to achieve a high accuracy of the simulations. Model simulations aided in explaining the effects arising from different shares of direct and diffuse radiation on canopy photosynthesis. This is a very important point to be further explored as diffuse radiation remains a part of light distribution and photosynthesis hardly studied in general; and, in particular, becomes more important with the increasing impact of shading. The simulation of the light availability, plant growth and yield formation within the strip of maize can be handled in a similar way as described for the smaller crop, bush bean. Modifications of the light model and a suitable plant growth model are presented and discussed. In conclusion, the main outcomes of this thesis indicate that the selection of cultivars adapted to the modified light environment have the largest potential to increase the productivity of strip-intercropped maize and bush bean. The most important characteristics of suitable maize cultivars include: (i) a high potential of kernel set; (ii) a higher water stress tolerance; and, (iii) reduced canopy height and LAI. The importance given to each of the components would subsequently be determined by the local weather and management conditions and the shade tolerance of the neighboring crop. On the other hand, to optimize yields of the smaller shaded crop, we present two options: (i) to modify the co-growing period of the intercrops temporarily to alleviate light competition during shade-sensitive growth stages; and, (ii) to modify the cropping design spatially and/or select different maize cultivars to reduce shading to the tolerated degree during the respective growth stage of the smaller crop. When the shade tolerance during the respective growth stages is determined, the light model developed can be used to optimize the cropping system temporarily and spatially. In this thesis, a promising approach, which combines a specific light partitioning model with process-oriented monocropping plant growth models, was developed. All models included in the approach can be applied at any location, and their generic nature also facilitates the integration of other crops. These attributes present a highly valuable contribution to intercropping research as their future optimization will depend strongly on the efficiency of the research efforts given: (i) the complexity of the underlying processes that determine the productivity; and, (ii) the minor share of time and money invested in intercropping research. Intercropping research has to prevent reinventing the wheel by identifying aspects in common with and already studied in monocropping systems and focus on aspects particularly inherent to intercropping systems.
Drought-induced processes in the rhizosphere of maize (Zea mays L.)
(2023) Käsbauer, Lena; Zörb, Christian
Drought events are increasing due to climate change, resulting in significant yield losses. Many breeding strategies focus on drought resistance to avoid these yield losses or complete crop failure. Additionally, to improve drought resistance under soil desiccation, the soil and particularly rhizosphere processes are more and more in the focus of research. Specifically, linkages between the diverse and highly dynamic interactions of soil, plant, and microorganism community must be understood. This thesis thus aims to answer the following research questions: i) Are root hairs relevant for water uptake, and what role do they play under drought? ii) Does local drought in Zea mays result in distinguishable systemic and local metabolic and physiological responses, as well as compensatory water uptake? iii) Do the physico-chemical properties of Zea mays mucilage differ between two common collection systems? In the first part, published studies considering root hairs in nutrient and water uptake were summarized, and show a high plasticity of root hairs under different nutrient and water availability states. This plasticity was apparent through changes in root hair morphology and development. Furthermore, the role of root hairs in water uptake is under discussion due to variable results from different studies and crop species. Nevertheless, it seems that overall root hairs improve drought resilience. Furthermore, a better nutrient uptake and mucilage exudation by root hairs and thus an increased drought stability is discussed. This suggests a beneficial role of root hairs for drought stress robustness. In the second part, local and systemic drought responses of maize and their effect on rhizosphere processes were assessed in a split-root experiment. The root system of maize was separated into two differently watered (watered, drought stressed) rhizobox chambers. The local drought treatment was performed for 10 days. Under these conditions, the local drought led to a local and systemic response through osmotic adjustment. Osmolarity increased in the shoot, while increased proline concentrations and slight changes in root exudates indicated a local response in the drought stressed root compartment. This metabolic adjustment contributed to a hydraulic redistribution of water between the root halves and enhanced water availability. Comparing the physico-chemical properties of maize mucilage collected by two common collection systems emphasized the impact of mucilage collection when interpreting the role of mucilage in rhizosphere processes. The mucilage differed in terms of physico-chemical properties, which included contact angle, viscosity, surface tension (physical) and nutrient content, pH, polysaccharide polymer length, and neutral sugar composition (chemical). The mucilage was collected in two ways: 1) from primary and seminal roots of seedlings growing in a semi-sterile aeroponic system and 2) from airborne brace roots of maize growing on sandy soil. The two collection systems differed in terms of plant age, environment (sterility, light availability, air humidity), and root type. The higher viscosity of the brace root mucilage may have reflected the drier air humidity surrounding the root and therefore the need to enhance water holding capacity. Non-sterile conditions during brace root mucilage collection probably resulted in higher shares of hexoses, while semi-sterile conditions may explain the lack of mannose in the aeroponic mucilage. Brace root mucilage may therefore have a greater relevance during soil desiccation than aeroponic mucilage. In summary, this work helps to fill knowledge gaps in understanding and linking rhizosphere processes by i) providing a state-of-the-art summary of root hair plasticity related to nutrient and water availability and concluding a beneficial role of root hairs in drought robustness, ii) showing local and systemic osmotic adjustment and hydraulic redistribution under local drought, and iii) emphasizing the role of the mucilage collection systems when interpreting the role of mucilage in rhizosphere processes
Effects of stand density and N fertilization on the performance of maize (Zea mays L.) intercropped with climbing beans (Phaseolus vulgaris L.)
(2022) Villwock, Daniel; Kurz, Sabine; Hartung, Jens; Müller-Lindenlauf, Maria
Maize is Germany’s most important fodder and energy crop. However, pure maize cultivation has ecological disadvantages. Moreover, its yield is low in crude protein, an important feed quality parameter. Maize–bean intercropping can potentially address both issues. A bean variety specially developed for intercropping was first introduced in 2016. Using this variety, a network of institutions conducted 13 field trials from 2017 to 2020 on four sites in Germany. We sought to determine the effects of stand density and nitrogen (N) fertilization on dry matter yield, crude protein yield, and soil mineral N content (Nmin) at harvest of intercropped vs. pure maize. The three intercropping bean densities we tested (7.5, 5.5, and 4 plants/m2) produced non-significantly different yields of dry matter or crude protein, given a maize density of 7.5–8 plants/m2. Intercropping was inferior to pure maize in dry matter yield, but non-significantly different in crude protein yield. Under neither cropping strategy were significant losses in dry matter or crude protein yield recorded with reduced compared to full N fertilization. At full fertilization, however, both pure maize systems and the 8/4 maize–bean intercrop system left significantly higher Nmin at harvest than the other variants of the corresponding system or N fertilization level and thus an increased risk of nitrate leaching. We encourage further optimization of yield performance in maize–bean intercropping, e.g., through breeding or promotion of biological N fixation via rhizobia inoculation. Furthermore, we recommend reducing N fertilization levels in maize cultivation.
Efficiency of phosphorus fertilizers derived from recycled biogas digestate as applied to maize and ryegrass in soils with different pH
(2022) Bach, Inga-Mareike; Essich, Lisa; Bauerle, Andrea; Müller, Torsten
Three phosphorus (P) fertilizer fractions recycled from biogas digestates were tested alone and in combination for their efficiency in two agricultural surface soils with different pH: a silty sandy loam and a clay loam. The experiments were carried out in pots under greenhouse conditions, using mineral triple superphosphate (TSP) as a reference. Maize was cultivated for 50 days, followed by ryegrass cultivation for an additional 84 days in the same soil, without additional fertilization. The variables investigated were above-ground plant biomass production, plant phosphorus concentration and content, and plant available phosphorus concentration in soil. The dry matter (DM) yield of maize was increased by the organic P fertilizers equal to or more than TSP in both soils. In the neutral soil, biomass was almost doubled compared to TSP when using one of the fractions (Struvite containing P-Salt) alone or in combination with dried solid fractions. P concentration in maize cultivated in the neutral soil was not significantly different between the P fertilization treatments. However, associated with biomass increase, the total P content in maize plants was equal to or higher than that with TSP. In the acidic soil, P concentration and total P content in maize plants, as well as the calcium-acetate-lactate extractable P (CAL-P) concentration in soil, were equal to or even higher than TSP. Ryegrass DM yield was unaffected by all P fertilizers, independent of the soil, although P concentration and total P content increased in the acidic soil with all fertilizers. Our results show that recycled P fertilizers from biogas digestates are effective P fertilizer alternatives to mineral TSP for maize cultivation under acidic and neutral soil conditions. The lack of growth effects in ryegrass indicates that recycled P fertilizers do not require changes in weed control. On the other hand, P extraction by ryegrass in overfertilized acidic soils as an option for soil remediation also works in soils fertilized with biogas digestate fractions.
External nutrition stimuli induced proteome and phosphoproteome responses of maize root hairs and arabidopsis root microsomal fraction
(2021) Li, Zhi; Schulze, Waltraud
This work studied how the proteome from young maize root hair cells responds to different nutrition deprivation, and gives perspectives to the possible involvement of NRT1.1 and NRT2.1 in regulating root membrane phosphoproteome responses. This work also proposes a phospho-switch model that may explain how the NRT2.1 activity was regulated.
Factors influencing the accuracy of genomic prediction in plant breeding
(2017) Schopp, Pascal; Melchinger, Albrecht E.
Genomic prediction (GP) is a novel statistical tool to estimate breeding values of selection candidates without the necessity to evaluate them phenotypically. The method calibrates a prediction model based on data of phenotyped individuals that were also genotyped with genome-wide molecular markers. The renunciation of an explicit identification of causal polymorphisms in the DNA sequence allows GP to explain significantly larger amounts of the genetic variance of complex traits than previous mapping-based approaches employed for marker-assisted selection. For these reasons, GP rapidly revolutionized dairy cattle breeding, where the method was originally developed and first implemented. By comparison, plant breeding is characterized by often intensively structured populations and more restricted resources routinely available for model calibration. This thesis addresses important issues related to these peculiarities to further promote an efficient integration of GP into plant breeding.
Gene mining in doubled haploid lines from European maize landraces with association mapping
(2014) Strigens, Alexander Carl Georg; Melchinger, Albrecht E.
Since the introduction of maize into Europe, open-pollinated varieties of flint maize were cultivated across the continent. Natural selection promoted adaptation to the climatic conditions prevailing in the different regions. With the advent of hybrid breeding in Europe during the 1950’s, some of the genes responsible for the specific adaptations of the landraces to abiotic and biotic stress were captured in the first developed inbred lines, but most of their genetic diversity is still untapped. Development of inbred lines out of this material by recurrent selfing is very tedious due to strong inbreeding depression. In contrast, the doubled-haploid (DH) technology allows producing fully homozygous lines out of landraces in only one step. This allows their precise characterization in replicated trials and identification of new genes by genome wide association (GWA) mapping. In this study we genotyped a set of 132 DH lines derived from European Flint landraces and 364 elite European flint (EU-F), European dent (EU-D) and North-American dent (NA-D) inbred lines with 56,110 single nucleotide polymorphism (SNP) markers. The lines were evaluated in field trials for morphologic and agronomic traits and GWA mapping was performed to identify underlying quantitative trait loci (QTL). In particular, our objectives were to (1) develop a robust method for quantifying early growth with a non-destructive remote-sensing platform, (2) evaluate the importance of early growth performance of inbred lines with regard to their testcross performance, (3) determine the potential of GWA mapping to identify genes underlying early growth and cold tolerance related traits, (4) evaluate the phenotypic and genotypic diversity recovered in the DH lines derived from the landraces, (5) estimate the effect of the DH method on the recovered genetic diversity, (6) identify new genes by GWA mapping in the DH lines derived from landraces, and (8) discuss the potential of DH lines derived from landraces to improve the genetic diversity and performance of elite maize germplasm. A phenotyping platform using spectral reflectance and light curtains was used to perform repeated measurements of biomass and estimate relative growth rates (RGR) of the DH and inbred lines, as well as of two testcrosses of 300 dent inbred lines. The DH lines derived from the landraces Schindelmeiser and Gelber Badischer had the highest RGR followed by EU-F lines, DH lines derived from Bugard, EU-D lines and, finally, NA-D lines. For inbred lines, whole plant dry matter yield (DMY) was positively correlated with RGR (r = 0.49), whereas this relation was weaker in the testcrosses (r = 0.29). RGR of the inbred lines correlated with RGR of their testcrosses (r = 0.42), but it had no influence on testcross DMY. A set of 375 EU-F, EU-D and NA-D lines were further evaluated in growth chambers under chilling (16/13°C) and optimal (27/25°C) temperatures. Photosynthetic and early growth performance were estimated for each treatment and an adaptation index (AI) built as the chilling to optimal performance ratio. Nineteen QTL were identified by GWA mapping for trait performance and AI. Candidate genes involved in ethylene signaling, brassinolide, and lignin biosynthesis were found in their vicinity. Several QTL for photosynthetic performance co-located with previously reported QTL and the QTL identified for shoot dry wieght under optimal conditions co-located with a QTL for RGR. Comparison of the DH lines derived from landraces with the EU-F lines showed that genotypic variances in single DH populations were greater than in the EU-F breeding population. A high average genetic distance among the DH lines derived from the same landrace as well as a rapid decay of linkage disequilibrium suggests a high effective population size of the landraces. Because no systematic phenotypic differences were observed between the landraces and synthetic landraces obtained by intermating the corresponding DH lines, the expected purge of lethal recessive alleles during the DH production did neither improve grain yield performance nor affect the recovered genetic diversity. Performing GWA in the DH lines derived from landraces as well as the EU-F, and EU-D lines allowed the identification of 49 QTL for 27 traits. A larger set of DH lines derived from more landraces might solve problems arising from population structure and allow a much higher power for the detection of new alleles. In conclusion, the introgression of DH lines derived from landraces into the elite breeding material would strongly broaden its genetic base. However, grain yield performance was 22% higher in EU-F lines than in the DH lines derived from landraces. Selection of the best DH lines would allow partially bridging this yield gap and marker-assisted selection may allow introgression of positive QTL without introducing negative features by linkage drag.
Genetic analysis of resistance to ear rot and mycotoxin contamination caused by Fusarium graminearum in European maize
(2012) Martin, Matthias; Melchinger, Albrecht E.
Maize is affected by a number of diseases. Among the various ear rots of maize, Gibberella ear rot (GER) caused by Fusarium graminearum is prevalent in Central Europe. This fungal pathogen produces secondary metabolites (mycotoxins), which adversely affect the health of humans and animals. Two important mycotoxins are the immunosuppressant deoxynivalenol (DON) and the mycoestrogen zearalenone (ZEA). The most efficient method to reduce mycotoxin contamination in maize is cultivation of resistant varieties. However, resistance breeding using classical phenotypic selection is laborious and time-consuming. Therefore, marker-assisted selection (MAS) may be a promising alternative to classical selection. Furthermore, for setting up a breeding program, knowledge about the relevance of the different modes of gene action and genotypic correlations among resistance and agronomic traits is required. The objectives of this study were to (1) estimate quantitative genetic parameters for GER severity and mycotoxin concentration in connected populations of doubled haploid (DH) lines, (2) map quantitative trait loci (QTL) for GER resistance and reduced mycotoxin contamination in these populations, (3) examine the congruency of QTL in these populations, (4) evaluate the prospects of using MAS to breed for GER resistance and reduced mycotoxin contamination, (5) estimate the genotypic correlation between the resistance of DH lines per se and the resistance of their testcrosses, (6) evaluate the influence of selection for increased resistance on agronomic performance of hybrids and (7) examine the relevance of different modes of gene action involved in the expression of the resistance in flint maize. Three field experiments were conducted, each of which comprised a different set of plant material. Experiment I comprised five DH line populations derived from the following F1 crosses among elite flint inbred lines: D152×UH006, D152×UH007, UH007×UH006, UH009×UH006 and UH009×UH007. Experiment II comprised testcross progenies of 94 DH lines and a dent single cross tester. Experiment III comprised the five F1 crosses, from which the DH populations had been derived, the F2 and the first backcross generations to the parents (BC1-P1, BC1-P2) as well as the two parent lines of each cross. Plants were artificially infected with spores of F. graminearum shortly after mid-silking using the silk channel inoculation technique. The DH lines were genotyped with simple sequence repeat (SSR) DNA markers, genetic linkage maps were constructed and QTL analyses were performed for resistance to GER, DON and ZEA contamination. Estimates of genotypic and genotype-by-environment interaction variances in Experiment I for GER severity and mycotoxin concentration were significant and heritabilities were moderately high to high in all populations. Thus, differences among DH lines for the resistance traits were mainly caused genetically and the resistance response varied depending on the environment. Owing to the effectiveness of artificial inoculation, the prospects are good to improve line resistance using a small number of test environments. QTL were detected in the four largest populations. Depending on the population, the mapped QTL together explained 21-51% of the genotypic variance for GER severity and 19-45% for DON concentration and 52% for ZEA concentration. Additive gene action was more important than digenic interactions of QTL, as indicated by the number of QTL having significant additive effects, their relative contributions to the total genotypic variance explained and the magnitude of their effects. Colocalized QTL for resistance to GER and mycotoxin contamination were identified in each mapping population. This was in agreement with strong genotypic correlations among these traits. QTL located at similar positions were detected across three populations in two chromosomal regions and across two populations in additional two regions. The results of this study indicated that a combination of classical phenotypic selection and MAS is a promising strategy for resistance breeding. In Experiment II, significant genotypic variation for resistance in lines and testcrosses showed that selection will be successful in both groups. Owing to low genotypic correlations between lines and testcrosses, however, resources should be mainly allocated to the evaluation of GER in testcrosses. Correlations of resistance with agronomic traits were weak or not significant. Therefore, selection for resistance and better agronomic performance can be carried out simultaneously. In Experiment III, generation means analysis indicated a prevalence of additive gene action for resistance. Significant dominance effects were found in only one cross for resistance to GER, but in four crosses for resistance to DON contamination. Owing to prevalence of additive gene action, the prospects are good to improve the resistance of the flint germplasm and to accumulate more favorable gene combinations in future breeding lines. Comparing the hybrid performance of flint×flint crosses of Experiment II and flint×dent crosses of Experiment III with their corresponding mid-parent performances indicated mid-parent heterosis for resistance. Therefore, prediction of hybrid performance based on performance of their parents will be possible only to a very limited extent. Future research should focus on fine mapping and validating of the detected QTL. For an efficient use of the QTL in a marker-assisted breeding program, knowledge about their effects in different genetic backgrounds is needed. Of particular importance are thereby the QTL effects in flint×dent crosses, which represent the preferred type of hybrid in Central European maize breeding programs.
Genetic dissection of hybrid performance and heterosis for yield-related traits in maize
(2021) Li, Dongdong; Zhou, Zhiqiang; Lu, Xiaohuan; Jiang, Yong; Li, Guoliang; Li, Junhui; Wang, Haoying; Chen, Shaojiang; Li, Xinhai; Würschum, Tobias; Reif, Jochen C.; Xu, Shizhong; Li, Mingshun; Liu, Wenxin
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
Genetic dissection of phosphorus use efficiency and genotype-by-environment interaction in maize
(2022) Li, Dongdong; Li, Guoliang; Wang, Haoying; Guo, Yuhang; Wang, Meng; Lu, Xiaohuan; Luo, Zhiheng; Zhu, Xintian; Weiß, Thea Mi; Roller, Sandra; Chen, Shaojiang; Yuan, Lixing; Würschum, Tobias; Liu, Wenxin
Genotype-by-environment interaction (G-by-E) is a common but potentially problematic phenomenon in plant breeding. In this study, we investigated the genotypic performance and two measures of plasticity on a phenotypic and genetic level by assessing 234 maize doubled haploid lines from six populations for 15 traits in seven macro-environments with a focus on varying soil phosphorus levels. It was found intergenic regions contributed the most to the variation of phenotypic linear plasticity. For 15 traits, 124 and 31 quantitative trait loci (QTL) were identified for genotypic performance and phenotypic plasticity, respectively. Further, some genes associated with phosphorus use efficiency, such as Zm00001eb117170, Zm00001eb258520, and Zm00001eb265410, encode small ubiquitin-like modifier E3 ligase were identified. By significantly testing the main effect and G-by-E effect, 38 main QTL and 17 interaction QTL were identified, respectively, in which MQTL38 contained the gene Zm00001eb374120, and its effect was related to phosphorus concentration in the soil, the lower the concentration, the greater the effect. Differences in the size and sign of the QTL effect in multiple environments could account for G-by-E. At last, the superiority of G-by-E in genomic selection was observed. In summary, our findings will provide theoretical guidance for breeding P-efficient and broadly adaptable varieties.
Genetic dissection of phosphorus use efficiency in a maize association population under two P levels in the field
(2021) Li, Dongdong; Wang, Haoying; Wang, Meng; Li, Guoliang; Chen, Zhe; Leiser, Willmar L.; Weiß, Thea Mi; Lu, Xiaohuan; Wang, Ming; Chen, Shaojiang; Chen, Fanjun; Yuan, Lixing; Würschum, Tobias; Liu, Wenxin
Genetic diversity, population structure, and linkage disequilibrium in the context of genome-wide association mapping of northern corn leaf blight resistance
(2012) van Inghelandt, Delphine; Melchinger, Albrecht E.
Besides linkage mapping, association mapping (AM) has become a powerful complement for understanding the genetic basis of complex traits. AM utilizes the natural genetic diversity and the linkage disequilibrium (LD) present in a diverse germplasm set. Setosphaeria turcica is a fungal pathogen that causes northern corn leaf blight (NCLB) in maize. The objective of this thesis research was to set the stage for and perform AM in elite maize breeding populations for NCLB resistance. Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of my study were to (i) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (ii) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (iii) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. The study was based on 1 537 elite maize inbred lines genotyped with 359 SSR and 8 244 SNP markers. My results indicated that both SSR and SNP markers are suitable for uncovering population structure. The same conclusions regarding the structure and the diversity of heterotic pools can be drawn from both markers types. However, fewer SSRs as SNPs are required for this goal, which facilitates the computations, for instance by the STRUCTURE software. Finally, the findings indicated that under the assumption of a fixed budget, modified Roger?s distances and gene diversity could be more precisely estimated with SNPs than with SSRs, and we proposed that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. Association mapping is based on LD shaped by historical recombinations. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of genomewide association mapping studies. The objectives of my study were to (i) examine the extent of LD with SSR and SNP markers in 1 537 commercial maize inbred lines belonging to four heterotic pools, (ii) compare the LD patterns determined by these two marker types, (iii) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (iv) investigate temporal trends of LD. The results suggested that SNP markers of the examined density, unlike SSR markers, can be used effectively for association studies in commercial maize germplasm. Based on the decay of LD in the various heterotic pools, between 4 000 and 65 000 SNP markers would be needed to detect with a reasonable power associations with rather large quantitative trait loci (QTL). The 60 K SNP chip currently available for maize seems appropriate to identify QTLs that explain at least 10% of the phenotypic variance. However, to identify QTLs with smaller effects, which is a realistic situation for most traits of interest to maize breeders, a much higher marker density is required. NCLB is a serious foliar disease in maize. In order to unravel the genetic architecture of the resistance against this disease, a vast association mapping panel comprising 1 487 European maize inbred lines was used to (i) identify chromosomal regions affecting flowering time (FT) and NCLB resistance, (ii) examine the epistatic interactions of the identified chromosomal regions with the genetic background on an individual molecular marker basis, and (iii) dissect the correlation between NCLB resistance and FT. We observed for FT, a trait for which already various genetic analyses have been performed in maize, a very well interpretable pattern of SNP associations, suggesting that data from practical plant breeding programs can be used to dissect polygenic traits. Furthermore, we described SNPs associated with NCLB and NCLB corrected for FT resistance that are located in genes for which a direct link to the trait is discernable or which are located in bins of the maize genome for which previously QTLs have been reported. Some of the SNPs showed significant epistatic interactions with markers from the genetic background. The observation that the listed SNPs and their epistatic interactions explained in the entire germplasm set about 10% and in some individual heterotic pools up to 30% of the genetic variance suggests that significant progress towards improving the resistance of maize against NCLB by marker-assisted selection is possible with these markers, without much compromising on late flowering time. Furthermore, these regions are interesting for further research to understand the mechanisms of resistance against NCLB and diseases in general, because some of the genes identified have not been annotated so far for these functions.
Genetic variation for cold tolerance in two nested association mapping populations
(2023) Revilla, Pedro; Butrón, Ana; Rodriguez, Víctor Manuel; Rincent, Renaud; Charcosset, Alain; Giauffret, Catherine; Melchinger, Albrecht E.; Schön, Chris-Carolin; Bauer, Eva; Altmann, Thomas; Brunel, Dominique; Moreno-González, Jesús; Campo, Laura; Ouzunova, Milena; Álvarez, Ángel; Ruíz de Galarreta, José Ignacio; Laborde, Jacques; Malvar, Rosa Ana
Cold reduces maize (Zea mays L.) production and delays sowings. Cold tolerance in maize is very limited, and breeding maize for cold tolerance is still a major challenge. Our objective was to detect QTL for cold tolerance at germination and seedling stages. We evaluated, under cold and control conditions, 919 Dent and 1009 Flint inbred lines from two nested association mapping designs consisting in 24 double-haploid populations, genotyped with 56,110 SNPs. We found a large diversity of maize cold tolerance within these NAM populations. We detected one QTL for plant weight and four for fluorescence under cold conditions, as well as one for plant weight and two for chlorophyll content under control conditions in the Dent-NAM. There were fewer significant QTL under control conditions than under cold conditions, and half of the QTL were for quantum efficiency of photosystem II. Our results supported the large genetic discrepancy between optimal and low temperatures, as the quantity and the position of the QTL were very variable between control and cold conditions. Furthermore, as we have not found alleles with significant effects on these NAM designs, further studies are needed with other experimental designs to find favorable alleles with important effects for improving cold tolerance in maize.
Genetic variation in early maturing European maize germplasm for resistance to ear rots and mycotoxin contamination caused by Fusarium spp.
(2010) Bolduan, Christof; Melchinger, Albrecht E.
Ear rots of maize, caused by Fusarium spp., are of major concern because they lead to losses in grain yield and contamination with mycotoxins which harm animals and humans. In the absence of other strategies, breeding maize for genetic resistance is currently the most promising avenue to control these rots and mycotoxin accumulation. The predominant pathogens in Central Europe are F. graminearum, the causative agent of Gibberella ear rot (GER), and F. verticillioides, the causative agent of Fusarium ear rot (FER). GER causes contamination with deoxynivalenol (DON), nivalenol and zearalenone (ZEA), whereas FER causes contamination with fumonisins (FUM). Information on the resistance to GER and FER and mycotoxin contamination is lacking for maize adapted to the cooler climatic conditions of Central Europe. In this study we investigated (1) the resistance of early maturing European elite inbred lines against GER and FER and contamination of mycotoxins, (2) the genetic variances and heritabilities for ear rot ratings and mycotoxin concentrations, (3) the correlations of ear rot ratings with mycotoxin concentrations, (4) the correlations between line per se (LP) and testcross performance (TP) for GER rating and DON concentration, (5) the aggressiveness of and mycotoxins produced by different isolates of F. graminearum and F. verticillioides, and (6) the potential of near infrared spectroscopy (NIRS) to estimate concentrations of DON and FUM in maize grains under artificial inoculation. Significant genotypic variances and moderate to high heritabilities were found for GER, DON and ZEA among the inbred lines and for GER and DON among the testcrosses, as well as for FER and FUM among the inbred lines. Further, genotype x environment interaction variances were significant for all traits except FUM. Thus, the results underlined the presence of ample genotypic variation and the need to conduct multi-environment tests for reliable identification of resistant genotypes. Ear rot ratings and mycotoxin production of eight isolates each of F. graminearum and F. verticillioides differed significantly. Even though, isolate x inbred interactions were significant only in the case of F. graminearum, and no rank reversals occurred among the tested inbred lines. Most isolates differentiated the susceptible inbreds from the resistant ones for severity ratings. However, the differences between the two groups were smaller for the less aggressive isolates. Therefore, we recommend using a single, environmentally stable and sufficiently aggressive isolate for resistance screenings under artificial inoculation. Strong correlations between ear rot severity and mycotoxin concentrations indicated that selection for low ear rot severity under artificial inoculation will result in high correlated selection response for low mycotoxin concentration, particularly for GER and DON. Selection for ear rot severity is less resource-demanding and quicker than selection for mycotoxin concentration. Thus, it enables the breeder to maximize selection gain for a given budget. However, the selected elite material should be evaluated for mycotoxin concentrations in order to avoid ?false positives?. In this regard, NIRS showed high potential to predict DON concentrations in grain obtained from artificially inoculated maize. Compared to the commonly employed ELISA assay, NIRS assays are considerably cheaper, because no mycotoxin extractions and test kits are needed. We observed moderate positive correlations between GER and FER, and identified inbreds combining resistance to both ear rots. Therefore, selection for resistance to one pathogen is expected to result in indirect response to the other. Nevertheless, in advanced stages of each breeding cycle, lines preselected for other agronomically important traits should be evaluated for resistance to both pathogens. Genotypic variances for GER and DON were generally higher in LP than TP. Thus, assuming identical selection intensities for each scheme, the expected response to selection for LP should be higher than for TP. However, owing to moderate correlations between LP and TP for GER and DON, selection based on LP is not sufficient, because the ultimate goal is to develop resistant hybrids. Therefore, a multi-stage selection procedure is recommended with evaluation of agronomically promising lines for GER in only one environment in order to eliminate highly susceptible lines, followed by evaluation of TP of the selected lines for GER with one tester of moderate to high resistance level from the opposite heterotic pool in two to three environments.