Browsing by Person "Stich, Benjamin"

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Genetic approaches to dissect iron efficiency in maize
(2015) Benke, Andreas; Stich, Benjamin
Maize is susceptible to severe Fe-deficiency symptoms when growing on soils with high pH. Therefore, development of Fe-efficient maize genotypes would aid to overcome Fe limitation on these soils. However, Fe-efficiency is a quantitative trait depending on complex mechanism interactions. The determination of these mechanisms would provide a better understanding of the complex trait Fe-efficiency. In the actual study, the determination of Fe-efficiency involved mechanisms were tackled by population and quantitative genetics. In fact, population genetics facilitate the discovery of genes being important to crop improvement based on a comparison of gene evolution and its ancestral genetic material. Linkage mapping and association analyses require both phenotypic variation and polymorphic markers to determine important quantitative trait loci (QTL). The objective of this research was to dissect the genetic architecture of Fe-efficiency in maize by applying different genetic approaches. Artificial selection during domestication and (or) crop improvement can result in limitation of sequence variation at candidate genes that could limit their detection by quantitative genetic approaches. The objectives of our study were to (i) describe patterns of sequence variation of 14 candidate genes for mobilization, uptake, and transport of Fe in maize, as well as regulatory function and (ii) determine if these genes were targets of selection during domestication. This study was based on 14 candidate genes sequences of 27 diverse maize inbreds, 18 teosinte inbreds, and one Zea luxurians strain as an outgroup. The experimental results suggested that the majority of candidate genes for Fe-efficiency examined in this study were not target of artificial selection. Nevertheless, the genes NAAT1, NAS1, and MTK coding for enzymes involved in phytosiderophore production, NRAMP3 responsible for Fe remobilization during germination, and YS1 transporting PS-Fe-complexes into the root showed signatures of selection. These genes might be important for the adaptation of maize to diverse environments with different Fe availabilities. This in turn suggests, that Fe-efficiency was an adaptive trait during maize domestication from teosinte. Identification of QTL provides information on the chromosomal locations contributing to the quantitative variation of complex traits. The benefit of QTL mapping compared to mutant screenings is the possibility to detect multiple genes which may be associated with the phenotypic trait. The objectives of our studies were to (i) identify QTLs for morphological and physiological traits related to Fe homeostasis, (ii) analyze Fe-dependent expression levels of genes known to be involved in Fe homeostasis as well as positional candidate genes from QTL analysis, and (iii) identify QTLs which control the mineral nutrient concentration difference. Our studies were based on experimental data of 85 genotypes from the IBM population cultivated in a hydroponic system. The QTL mapping of morphological and physiological traits provided new putative candidate genes like Ferredoxin 1, putative ferredoxin PETF, MTP4, and MTP8 which complement the genes already known as being responsible for efficient Fe homeostasis at both, deficient and sufficient Fe regime. Furthermore, the candidate gene expression indicated a trans-acting regulation for DMAS1, NAS3, NAS1, FDH1, IDI2, IDI4, and MTK. The mineral element trait QTL confidence intervals comprised candidate genes that sequestrate Cd in vacuoles (HMA3), transport Fe2+into the root cells (ZIP10), protect the cell against oxidative stress (glutaredoxin), ensure micro nutrient homeostasis during sufficient iron regime (NRAMP2), regulate protein activities (PP2C), and prevent deleterious accumulation and interaction of specific elements within cells (PHT1;5, ZIP4). Association mapping is promising to overcome the limitations of low allele diversity and absent recombinations events causing poor resolution in detecting QTL by linkage mapping. In order to unravel the genetic architecture of Fe-efficiency a vast association mapping panel comprising 267 maize inbred lines was used to (i) detect polymorphisms affecting the morphological/physiological trait formation and (ii) fine map QTL confidence intervals determined according to linkage mapping. Some of the SNPs located beyond coding regions of genes that might be important cis-binding-sites for transcription factors. Furthermore, genes detected at the Fe-deficient regime indicate to be involved in universal stress response. However, genes linked to SNPs detected at Fe-sufficient regime might comprise alleles of Fe inefficient genotypes causing inferior trait expression. The combination of several approaches provided a valuable resource of candidate genes which might aid to increase our understanding of the mechanisms of Fe-efficiency in maize and foster the efforts in breeding superior cultivars by applying molecular marker techniques.
Inheritance of Barley yellow dwarf virus resistance in maize
(2015) Horn, Frederike; Stich, Benjamin
Barley yellow dwarf (BYD) is one of the economically most important virus diseases in cereals. Due to increasing winter temperatures it is expected that BYD will become an increasing problem in maize cultivation. In earlier studies, it was reported that BYD has a negative impact on plant performance of maize. BYD virus (BYDV) is transmitted by aphids and the best control of the virus is the development of resistant maize cultivars. Therefore, the first objectives of my thesis research were to (i) determine phenotypic and genotypic variation in five segregating populations and in a broad germplasm set of maize with respect to BYDV tolerance and resistance as well as to (ii) quantify the influence of BYDV infection on the plant traits plant height, ear height, and flowering time. I observed a negative impact of BYDV infection on maize plant traits which shows that the development of resistant maize cultivars is of high importance for maize cultivation. Furthermore, in the connected biparental populations as well as in the association mapping population, I observed a high genotypic variance with regard to BYDV resistance which is the requirement for successful breeding and the identification of genome regions which contribute to BYDV resistance. The evaluation of BYDV resistance by the inoculation with BYDV and by double antibody sandwich enzyme-linked immunosorbent assay (DASELISA) is dificult to be included in the breeding process. Therefore, molecular markers are of high importance for the improvement of BYDV resistance by breeding. Therefore, the objective of this study was the (iii) identification of genome regions which are involved in the BYDV resistance by a genome wide association study (GWAS). For the BYDV resistance traits, significantly (α=0.01) associated SNPs were identified in the GWAS on chromosome 10 and 4. The SNPs identified for virus extinction on chromosome 10 explained in a simultaneous fit 25% of the phenotypic variance and were located in gene regions which were in other plants described to be involved in resistance mechanisms. This suggests that BYDV resistance is inherited oligogenically and that genes involved in general resistance mechanisms are also involved in BYDV resistance in maize. GWAS has the advantage that a large number of alleles per locus can be surveyed simultaneously, and because historical recombinations can be used, the mapping resolution is higher compared to classical linkage mapping. Nevertheless, genes contributing to phenotypic variation which show a low allele frequency can remain undetected. Due to a balanced allele frequency in segregating populations, linkage mapping has the advantage of higher QTL detection power compared to GWAS. Therefore, the objective of this study was to (iv) validate the genome regions with a linkage analysis in connected biparental crosses. The genome region on chromosome 10 which was identified in the GWAS to be linked to BYDV resistance could be validated in the linkage mapping study with connected populations as well as in the single populations. Furthermore, the QTL on chromosome 10 colocalized with the QTL identified in controlled greenhouse conditions. In earlier studies, QTL for other virus resistances were identified on chromosome 10. This suggests that these genes are involved in multiple virus resistances. The identified genome regions explain 45% of the phenotypic variance and are, therefore, promising for the use in MAS. The broad genotypic variation with regard to BYDV resistance, observed in my thesis research, provided a good basis for the successful identification of molecular markers which are associated with BYDV resistance in maize. The markers identified in my study by GWAS were validated by a linkage mapping approach and are promising for the use in marker assisted selection on BYDV resistance in maize breeding.
Linkage disequilibrium and association mapping in elite germplasm of European maize
(2006) Stich, Benjamin; Melchinger, Albrecht E.
Linkage mapping has become a routine tool for the identification of quantitative trait loci (QTL) in plants. An alternative, promising approach is association mapping, which has been successfully applied in human genetics to detect QTL coding for diseases. The objectives of this research were to examine the feasibility of association mapping in elite maize breeding populations and develop for this purpose appropriate biometric methods. The feasibility of association mapping depends on the extent of linkage disequilibrium (LD) as well as on the forces generating and conserving LD in the population under consideration. The objectives of our studies were to (i) examine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) marker loci, (ii) compare these results with those obtained with amplified fragment length polymorphism (AFLP) markers, and (iii) investigate the forces generating and conserving LD in plant breeding populations. Our studies were based on experimental data of European elite maize inbreds as well as on computer simulations modeling the breeding history of the European flint heterotic group. The experimental results on European elite maize germplasm suggested that the extent of LD between SSR markers as well as AFLP markers are encouraging for the detection of marker-phenotype associations in genomewide scans. In populations with a short history of recombination, SSRs are advantageous over AFLPs in that they have a higher power to detect LD. In contrast, in populations with a long history of recombination, for which no LD is expected between pairs of SSR markers, AFLP markers should be favored over SSRs because then their higher marker density that is generated with a fixed budget can be used. Furthermore, the results of our experimental and simulation studies indicated that not only physical linkage is a cause of LD in plant breeding populations, but also relatedness, population stratification, genetic drift, and selection. So far, in plant genetics the logistic regression ratio test (LRRT) has been applied as a population-based association mapping approach. However, this test does only correct for LD caused by population stratification. The objectives of the presented study were to (i) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs and (ii) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) and the commonly employed LRRT with respect to the power and type I error rate of QTL detection. This study was based on computer simulations modeling the breeding history of the European maize heterotic groups. In QIPDT the power of QTL detection was higher with 75 extended pedigrees than in LRRT with 75 independent inbreds. Furthermore, while the type I error rate of LRRT surpassed the nominal ® level, the QIPDT adhered to it. These results suggested that the QIPDT is superior to the LRRT for genome-wide association mapping if data collected routinely in plant breeding programs are available. Epistatic interactions among QTL contribute substantially to the genetic variation in complex traits. The main objectives of our study were to (i) investigate by computer simulations the power and proportion of false positives for detecting three-way interactions among QTL involved in a metabolic pathway in populations of recombinant inbred lines (RILs) derived from a nested design and (ii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The computer simulations of this study were based on single nucleotide polymorphism haplotype data of 26 diverse maize inbreds. The power and proportion of false positives to detect three-way interactions with 5000 RILs derived from a nested design was relatively high for both the 4 QTL and the 12 QTL scenario. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distancebased designs than for RILs derived from a nested or diallel design. Our results suggested that association mapping methods adapted to the special features of plant breeding populations have the potential to overcome the limitations of classical linkage mapping methods.
The genetic basis of heat tolerance in temperate maize (Zea mays L.)
(2016) Frey, Felix P.; Stich, Benjamin
The global mean temperature and probability of heat waves are expected to increase in the future, which has the potential to cause severe damages to maize production. To elucidate the genetic mechanisms of the response of temperate maize to heat stress and for the tolerance to heat stress, in a first experiment I applied gene expression profiling. Therewith, I investigated the transcriptomic response of temperate maize to linearly increasing heat levels. Further, I identified genes associated with heat tolerance in a set of eight genotypes with contrasting heat tolerance behavior. I identified 607 heat responsive genes, which elucidate the genetic pathways behind the response of maize to heat stress and can help to expand the knowledge of plant responses to other abiotic stresses. Further, I identified 39 genes which were differentially regulated between heat tolerant and heat susceptible inbreds and, thus, are putative heat tolerance candidate genes. Two of these candidate genes were located in genome regions which were associated with heat tolerance during seedling and adult stage that have been detected in QTL studies in the frame of this thesis. Their exact molecular functions, however, are still unknown. The statistical approach to identify heat tolerance genes, presented in my thesis, enables researchers to investigate the transcriptomic response of multiple genotypes to changing conditions across several experiments, considering their natural variation for a quantitative trait. In order to develop more heat tolerant cultivars, knowledge of natural variation for heat tolerance in temperate maize is indispensable. Therefore, heat tolerance was assessed in a set of intra- and interpool Dent and Flint populations on a multi-environment level. Usually, heat stress in temperate Europe occurs during the adult stage of maize. However, as maize is of increasing importance as a biogas crop, farmers can reduce the growth period by postponed sowing after the harvest of the winter cereals in early summer and, thus, sensitive maize seedlings can be exposed to heat stress. Therefore, I aimed to assess heat tolerance in six connected segregating Dent and Flint populations during both developmental stages considering besides multiple environments also multiple traits. At heat stress, I observed an average decrease of 20% of the shoot dry weight during seedling stage and an average of 50% of yield loss, when heat stress was present during adult stage. At the heat locations heat stress was present in the year, when the experiments were conducted as temperatures exceeded 32°C there for more than 400 hours during the growing period in contrast to less than 30 hours at the standard locations. This emphasizes that maize crop production can suffer with the increasing number and intensity of summer heat waves. Furthermore, the study revealed strong differences between genotypes, which was indispensable to differentiate between heat tolerant and heat susceptible inbred lines. The tested genotypes originating from the Flint pool turned out to possess higher heat tolerance during seedling stage, whereas the genotypes derived from the Dent pool possessed higher heat tolerance during adult stage. This fact could be exploited by the maintenance of two pools with contrasting heat tolerance and could be beneficial for hybrid breeding. A direct selection of more heat tolerant genotypes in terms of grain yield is expensive and time-consuming. To facilitate the selection process in order to develop more heat tolerant cultivars, breeders could make use of marker assisted selection. To lay the foundation for this technique, in my thesis, QTL for heat tolerance during adult and during seedling stage were identified with the previously mentioned populations. Two QTL explained 19% of the total variance for heat tolerance with respect to grain yield in a simultaneous fit. Furthermore each two QTL were identified for two principal components, which accounted for heat tolerance during seedling stage. They explained 14 and 12% of the respective variance. The results can be used by breeding companies to develop marker assays in order to select heat tolerant genotypes from their proprietary genetic material during both stages in an initial screening. This would reduce the field capacities considerably, which are needed to test heat tolerance on a field level.