Browsing by Subject "Assoziationskartierung"

Now showing 1 - 8 of 8

Bridging genomics and genetic diversity : association between sequence polymorphism and trait variation in a spring barley collection
(2009) Haseneyer, Grit; Geiger, Hartwig H.
Association analysis has become common praxis in plant genetics for high-resolution mapping of quantitative trait loci (QTL), validating candidate genes, and identifying important alleles for crop improvement. In the present study the feasibility of association mapping in barley is investigated by associating DNA polymorphisms in selected candidate genes with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. (1) As a starting point a worldwide collection of spring barley (Hordeum vulgare L.) accessions has been established to serve as an association platform for the present and possible further studies. This collection of 224 accessions, sampled from the IPK genebank, consists of 109 European, 45 West Asian and North African, 40 East Asian and 30 American entries. Forty-five EST derived polymorphic SSRs were used to determine the genetic structure. The markers were equally distributed over all seven chromosomes. Phenotypic data were assessed in field experiments performed at three locations in 2004 and 2005 in Germany. (2) Seven candidate genes were considered. Fragments of these genes were amplified and sequenced in the established collection. Single nucleotide polymorphisms (SNPs), haplotype variants, and linkage disequilibrium (LD) were investigated. (3) One gene was additionally analysed in 42 bread wheat (Triticum aestivum L.) accessions in order to compare barley and wheat for nucleotide diversity and LD. (4) Association analysis between SNPs and haplotype variants of the selected candidate genes and the phenotypic variation in thousand-grain weight, crude protein content, starch content, plant height, and flowering time was used to identify candidate genes influencing the variation of these traits in spring barley. A mixed model association-mapping method was employed for this purpose. In the established collection, significant genotypic variation was observed for all traits under study. Genotype×environment interaction variances were much smaller than the genotypic variances and heritability coefficients exceeded 0.9. Statistical analyses of population stratification revealed two major subgroups, mainly comprising two-rowed and six-rowed accessions, respectively. Within the sequenced fragments (13kb) of the seven candidate genes, 216 polymorphic sites and 93 haplotypes were detected demonstrating a moderate to high level of nucleotide and haplotype diversity in the germplasm collection. Most haplotypes (74.2%) occurred at a low frequency (<0.05) and therefore were rejected in the candidate gene-based association analysis. Pair-wise LD estimates between the detected SNPs revealed different intra-gene linkage patterns. The 45 SSR markers used for analysing the population structure revealed low intra- and interchromosomal LD (r²<0.2). Significant marker-trait associations between the candidate genes and the respective target traits were identified. The barley and wheat genes showed a high level of nucleotide identity (>95%) in the coding sequences, the distribution of polymorphisms was also similar in the two species, and both map to a syntenic position on chromosome 3. However, the genes were different in both collections with respect to LD and Tajima?s D statistic. In the barley collection only a moderate level of LD was observed whereas in wheat, LD was absolute between polymorphic sites located in the first intron while it decayed by distance between the former sites and those located downstream the first intron. Differences in Tajima?s D values indicate a lower selection pressure on the gene in barley than in wheat. In conclusion, the established association platform represents an excellent resource for marker-trait association studies. The germplasm collection displays a wide range of genotypic and phenotypic diversity providing phenotypic data for economically important traits and comprehensive information about the nucleotide and haplotype polymorphism of seven candidate genes. Association results demonstrate that the candidate gene-based approach of association mapping is an appropriate tool for characterising gene loci that have a significant impact on plant development and grain quality in spring barley.
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.
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.
Genome-wide association mapping of molecular and physiological component traits in maize
(2013) Riedelsheimer, Christian; Melchinger, Albrecht E.
Genome-wide association (GWA) mapping emerged as a powerful tool to dissect complex traits in maize. Yet, most agronomic traits were found to be highly polygenic and the detected associations explained together only a small portion of the total genetic variance. Hence, the majority of genetic factors underlying many agronomically important traits are still unknown. New approaches are needed for unravelling the chain from the genes to the phenotype which is still largely unresolved for most quantitative traits in maize. Instead of further enlarging the mapping population to increase the power to detect even smaller QTL, this thesis research aims to present an alternative route by mapping not the polygenic trait of primary interest itself, but genetically correlated molecular and physiological component traits. As such components represent biological sub-processes underlying the trait of interest, they are supposed to be genetically less complex and thus, more suitable for genetic mapping. Using large diversity panels of maize inbred lines, this approach is demonstrated with (i) biomass yield by using metabolites and lipids as molecular component traits and with (ii) chilling sensitivity by using physiological component traits such as photosynthesis parameters derived from chlorophyll fluorescence measurements. In a first step, we developed a sampling and randomization scheme which allowed us to obtain metabolic and lipid profiles from large-scale field trials. Both profiles were found to be inten- sively structured reflecting their functional grouping. They also showed repeatabilities higher than in comparable profiles obtained in previous studies with the model plant Arabidopsis under controlled conditions. By applying GWAS with 56,110 SNPs to metabolites and lipids, large-scale genetic associations explaining more than 30 % of the genetic variance were detected. Confounding with structure was found to be a problem of less extent for molecular components than for agronomic traits like flowering time. The lipidome was also found to show a multilevel control architecture similar as employed in controlling complex mechanical systems. In several instances, direct links between candidate genes underlying the detected associations and agronomic traits could be established. An example is cinnamoyl-CoA reductase, a key enzyme in the lingin biosynthesis pathway. It was found to be a candidate gene underlying a major QTL found for several intermediates in the lignin biosynthesis pathways. These intemediates were in turn found to be correlated with plant height, lignin content, and dry matter yield at the end of the vegetation period. The different signs of these correlations indicated that the relationships between pathway intermediates and the final product is not simple. Directly modeling complex traits with individual component traits may therefore require consideration of feedback loops and other interdependencies. Such connections were however found difficult to be established with physiological components underlying chilling sensitivity. The main reasons for this were the weak correlations between physiological components under controlled conditions and chilling sensitivity in the field as well as high levels of genotype × environment interactions caused by the complex and environment- dependent responses of maize after perception of chilling temperatures. The approach explored in this thesis research uses component traits to gain biological insights about the genetic control of biomass yield and chilling sensitivity evaluated in diverse populations of still manageable sizes. We showed that GWAS with 56k SNPs can identify large additive effects for component traits correlated with these traits. For mapping epistatic interactions and rare variants, classical linkage mapping with biparental populations will be a reasonable complementary approach. However, controlling and modeling genotype × environment interactions remains an important issue for understanding the genetic basis of especially chilling sensitivity. If the goal is merely to predict the phenotypic value in a given set of en- vironments, black-box genomic selection methods with either SNPs, molecular profiles, or a combination of both, are very promising strategies to achieve this goal.
Improving host resistance to Fusarium head blight in wheat (Triticum aestivum L.) and Gibberella ear rot in maize (Zea mays L.)
(2023) Akohoue, Félicien; Miedaner, Thomas
Fusarium head blight (FHB) in wheat and Fusarium (FER) and Gibberella ear rot (GER) in maize are major cereal diseases which reduce yield and contaminate kernels with several mycotoxins. In Europe, these diseases contribute to significant yield gaps and high mycotoxin risks across countries. However, existing management strategies related to agronomic practices are not fully effective, with some of them being cost-prohibitive. Enhancing host plant resistance is additionally required for managing the diseases more effectively and sustainably. Unfortunately, breeding for FHB resistance is challenged by complex interactions with morphological traits and the quantitative nature of the trait. In maize, available genetic resources have not been fully exploited to improve GER resistance in elite materials. In this work, we elucidated the complex interactions between FHB resistance and morphological traits, like plant height (PH) and anther retention (AR) in wheat. The effect of reduced height (Rht) gene Rht24 on AR and the contribution of genomic background (GB) to FHB resistance in semi-dwarf genotypes were also assessed. GB refers to all genomic loci, except major Rht genes, that affect the traits. To achieve this, 401 winter wheat cultivars were evaluated across five environments (location × year combination). All cultivars were genotyped using Illumina 25 K Infinium single-nucleotide polymorphism array. We performed correlation and path coefficient analysis, and combined single and multi-trait genome-wide association studies (GWAS). Our findings revealed significant genotypic correlations and path effects between FHB severity with PH and AR, which were controlled by several pleiotropic loci. FHB severity and PH shared both negatively and positively acting pleiotropic loci, while only positively acting pleiotropic loci were detected between FHB severity and AR. Rht-D1 is a major pleiotropic gene which exerted a negative effect on FHB resistance. These pleiotropic loci contribute to our understanding of the complex genetic basis of FHB resistance, and their exploitation can help to simultaneously select for FHB resistance with PH and AR. Contrary to Rht-D1b, Rht24b had no negative effect on FHB resistance and AR. This exhibits Rht24 as an important FHB-neutral Rht gene which can be integrated into breeding programs. Genomic estimated breeding values (GEBV) were calculated for each cultivar to assess GB. We observed highly negative GEBV for FHB severity within resistant wheat cultivars. Susceptible cultivars exhibited positive GEBV. Genomic prediction has a great potential and can be exploited by selecting for semi-dwarf winter wheat genotypes with higher FHB resistance due to their genomic background resistance. To tackle maize ear rot diseases, refined and stable quantitative trait loci (QTL) harboring candidate genes conferring resistances to FER and GER were identified. The effectiveness of introgression of two European flint landraces, namely “Kemater Gelb Landmais” (KE) and “Petkuser Ferdinand Rot” (PE) was evaluated. The prediction accuracy of using line performance as a predictor of hybrid performance for GER resistance was also evaluated within the two landraces. We applied a meta-QTL (MQTL) analysis based on 15 diverse SNP-based QTL mapping studies and performed gene expression analysis using published RNA-seq data on GER resistance. In total, 40 MQTL were identified, of which 14 most refined MQTL harbored promising candidate genes for use in breeding programs for improving FER and GER resistances. 28 MQTL were common to both FER and GER, with most of them being shared between silk (channel) and kernel resistances. This highlights the co-inheritance of FER and GER resistances as well as types of active resistance. Resistance genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted breeding strategies. Afterwards, four GER resistant doubled haploid (DH) lines from both KE and PE landraces were crossed with two susceptible elite lines to generate six bi-parental populations with a total of 534 DH lines which were evaluated for GER resistance. GER severity within the six landrace-derived populations were reduced by 39−61% compared to the susceptible elite lines. Moderate to high genetic advance was observed within each population, and the use of KE landrace as a donor was generally more effective than PE landrace. This shows promise in enhancing resistance to GER in elite materials using the European flint landraces as donors. Furthermore, per se performance of 76 DH lines from both landraces was used to predict GER resistance of their corresponding testcrosses (TC). Moderate phenotypic and genomic prediction accuracy between TC and line per se performance was found for GER resistance. This implies that pre-selecting lines for GER resistance is feasible; however, TC should be additionally tested on a later selection stage to aim for GER-resistant hybrid cultivars.
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.
Phenotypic and genotypic assessment of traits with relevance for hybrid breeding in European winter wheat
(2015) Langer, Simon Martin; Würschum, Tobias
Hybrid breeding in wheat has recently received increased interest, especially in Europe, and large public and private projects investigating hybrid wheat breeding have been launched. Hybrid breeding has been a great success story for allogamous crops and is seen as a promising approach to increase the yield potential in wheat. Wheat covers more of the world’s surface than any other food crop and is the second main staple crop for human consumption. It can be produced under widely varying conditions and is grown all around the globe, yet, yield gain has declined and is lagging behind the needs of the constantly growing human population. Future challenges in wheat breeding such as the establishment of hybrid varieties and the adaptation of breeding germplasm to increasing stresses caused by climatic changes also in Europe require knowledge-based improvements of relevant traits and phenotyping approaches suited for applied high-throughput plant breeding. A major limitation for the establishment and the production of hybrid wheat is the lack of a cost-efficient hybrid seed production system. This requires the generation of parental ideotypes which maximize the cross-fertilization capability. Male parents should have an extended time of flowering, extrude anthers and widely shed large amounts of viable pollen. Females need increased receptivity for male pollen by opening the glumes and extruding stigmatic hair. Furthermore, male plants should be taller than females and a synchronized timing of flowering between the two parents is also of utmost importance. Employing a set of European elite winter wheat lines, we developed and evaluated phenotyping methods for important floral and flowering traits with relevance for improved cross-pollination (Publication I). We observed high heritabilities for important traits such as ‘pollen mass’ (h2=0.72) and ‘anther extrusion’ (h2=0.91). In addition, genotypic variances were significant which warrants further breeding success. Positive correlations were found among important flowering and floral characteristics which enables the improvement of outcrossing by indirect selection. ‘Pollen mass’ for example, was associated with ‘anther extrusion’, ‘anther length’ and ‘plant height’. Our findings suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross-fertilization. We investigated the genetic architecture of flowering time and plant height (Publication II and III). A panel of 410 European winter wheat varieties was genotyped by a genotyping-by-sequencing approach and in addition, analyzed for the effects of specific candidate genes. The major factor affecting flowering time was the photoperiod regulator Ppd-D1 (58.2% of explained genotypic variance) followed by Ppd-B1 copy number variation (3.2%). For plant height, the two candidate loci Rht-D1 (37.0%) and Rht-B1 (14.0%) had the largest effects on the trait but contrary to reports in the literature did not contribute to flowering time control. In addition, we identified several small effect QTL and epistatic QTL responsible for fine-adjustments of these two traits. Population structure and genetic relatedness in European elite wheat lines was assessed using different types of markers (Publication IV). Results for relatedness differed for the marker types but consistently showed the absence of a major population structure. Regarding the large wheat genome our results revealed that a high number of markers is necessary as there are regions with only low coverage. Concordantly, we were not able to identify the major flowering locus Ppd-D1 without targeted candidate gene analysis. Observations on the findings on population structure could be confirmed in Publication II and III and in addition, the geographical distribution of important flowering time and plant height genes displayed the historical development of wheat breeding in Europe. This information on genetic relatedness among lines can also be employed to assist the establishment of hybrid wheat.
Utilization of landraces of European flint maize for breeding and genetic research
(2023) Renner, Juliane; Melchinger, Albrecht E.
Mais ist eine der wichtigsten Kulturarten für die Landwirtschaft weltweit. Seit seiner Domestikation bildeten Landrassen den traditionellen Sortentyp. Durch Selektion und genetische Faktoren entstand eine breite Diversität an panmiktisch vermehrten Populationen, die gut an lokale Bedingungen angepasst waren. Dies änderte sich mit der Einführung der Hybridzüchtung, als nahezu alle Landrassen in der landwirtschaftlichen Produktion und als Ausgangsmaterial für die Züchtung verschwanden. Molekulare Analysen zeigen eine enge genetische Basis des Flint Pools im Vergleich zum Dent Pool. Genetische Ressourcen im Mais gehören zu den umfangreichsten aller Nutzpflanzen. Die Nutzung dieses bislang ungenutzten Reservoirs an genetischer Diversität in Landrassen bietet eine Möglichkeit, um der fortschreitenden Einengung der genetischen Basis entgegenzuwirken und somit den Aufgaben der Pflanzenzüchtung im Hinblick auf eine wachsende Weltbevölkerung sowie den Herausforderungen des Klimawandels und reduzierten Inputs im Anbau gerecht zu werden. Übergeordnetes Ziel dieser Studie war die Evaluierung europäischer Flint-Mais Landrassen, um deren genetische Vielfalt nutzen zu können. Im Speziellen waren die Ziele (i) die Variation in Testkreuzungen europäischer Mais-Landrassen zu bestimmen; (ii) die phänotypische und genotypische Variation der Linien innerhalb und zwischen Landrassen zu beurteilen; (iii) die Eigenleistung dieser Linien mit Elite-Linien sowie Founder-Linien aus dem europäischen Flint-Pool zu vergleichen; (iv) das Potential von doppelhaploiden (DH) Linien aus Landrassen im Vergleich zum Elitematerial für die Züchtung zu analysieren, um die enge genetische Basis des Flint-Pools zu erweitern; (v) die Verwendung von DH-Bibliotheken aus Landrassen für die Assoziationskartierung bis hin zur Eingrenzung kausaler Gene zu demonstrieren; und (vi) Schlussfolgerungen und Leitlinien für die Züchtung und Forschung zu erörtern , um DH-Linien aus Landrassen nutzbar zu machen. In einem ersten Versuch wurde eine umfangreiche Kollektion von 70 europäischen Flint-Landrassen mehrortig in Kombination mit zwei Elite Dent-Testern auf ihre Testkreuzungsleistung hin untersucht. Verglichen mit dem Ertrag moderner Hybriden war der Kornertrag der Testkreuzungen der Landrassen im Durchschnitt um 26 % geringer, jedoch wurde eine hohe genotypische Varianz zwischen den Landrassen für alle Merkmale beobachtet. Die Korrelationen waren mittel bis hoch für die meisten Merkmalskombinationen und entsprachen denen im Elitezuchtmaterial. Die genetische Korrelation der beiden Testkreuzungsserien überstieg 0,74 für alle Merkmale. Dies zeigt, dass es ausreicht die Leistung von Testkreuzungen in Kombination mit einem oder zwei Testern - bestehend aus Einfachkreuzungen des anderen Gen-Pools – zu bewerten, um das Potenzial von Landrassen für die Züchtung zu beurteilen. In einem zweiten Versuch produzierten wir Bibliotheken von DH-Linien der vielversprechendsten Landrassen des vorigen Versuches. Insgesamt wurden 389 DH-Linien aus sechs europäischer Flint Landrassen zusammen mit vier Flint Founder-Linien und 53 Elite Flintlinien auf 16 agronomische Merkmale an vier Standorten geprüft. Die genotypische Varianz (σ^2G) innerhalb der DH-Bibliotheken war größer als die zwischen den Bibliotheken und übertraf auch σ^2G der Elite Flintlinien. Darüber hinaus variierten die Mittelwerte und σ^2G zwischen den DH-Bibliotheken, was zu großen Unterschieden im Brauchbarkeits-Kriterium („usefulness“) führte. Der mittlere Kornertrag der Elite Flintlinien übertraf den der Flint Founder-Linien um 25 % und der DH-Bibliotheken um 62 %, was auf den beträchtlichen Zuchtfortschritt im Elitematerial hinweist sowie auf die erhebliche genetische Bürde, welche in den DH-Bibliotheken vorliegt. Die Brauchbarkeit der besten DH-Linien war trotzdem für viele Merkmale, einschließlich dem Kornertrag, mit der von Elite Flintlinien vergleichbar. Dies zeigt das enorme Potenzial, Landrassen zur Verbreiterung des genetisch engen Elite Flint-Pools zu verwenden. In einem dritten Versuch wurden das genetische Material des vorherigen Versuches mit dem MaizeSNP50 BeadChip von Illumina® genotypisiert und Samen aller Genotypen zur Extraktion und Analyse von 288 Metaboliten mit GC-MS verwendet. Sowohl die agronomischen Merkmale als auch die Metabolit-Daten wurden für eine Assoziationskartierung verwendet. Der schnelle Abfall des Kopplungsungleichgewichts benachbarter Marker in den DH-Bibliotheken im Vergleich zu den Elite Flintlinien führte zu einer hervorragenden Auflösung in der QTL-Kartierung, was durch die Feinkartierung eines QTL (= quantitative trait locus) für Ölgehalt bis zur Phenylalanin Insertion F469 in DGAT1-2 als kausale Variante demonstriert werden konnte. Darüber hinaus wurden für den Metaboliten Allantoin, der im Zusammenhang mit abiotischem Stress steht, Promotorpolymorphismen sowie die Expression einer Allantoinase als vermutete Ursache der Variation identifiziert. Dies gelang trotz der moderaten Größe der Kartierungspopulation. Diese Ergebnisse sind ermutigend, um DH-Bibliotheken von Landrassen für die Assoziationskartierung zu verwenden und QTL bis auf die kausalen Varianten zu entschlüsseln. Eine Erweiterung der Populationsgrößen der DH-Bibliotheken, ähnlich wie sie in anderen Versuchsdesigns in der Literatur verwendet wurden, ist hierbei zu empfehlen, um mit diesem Ansatz QTL zu detektieren, welche lediglich einen kleinen Teil der genetischen Varianz erklären. Dies eröffnet neue Wege zur Nutzung natürlicher und/oder neu geschaffener Allele in der Züchtung. Zusammenfassend zeigen die Ergebnisse dieser Arbeit, dass die genetische Variation europäischer Landrassen bei Flint-Mais eine einzigartige Quelle darstellt, um die fortschreitende Verengung der genetischen Basis des Elitematerials in diesem Gen-Pool umzukehren. Um vielversprechende Landrassen zu identifizieren, schlagen wir folgenden zweistufigen Ansatz vor: (i) Basierend auf der Bewertung der molekularen Diversität werden etwa hundert Landrassen in Leistungsprüfungen auf ihre Anpassungsfähigkeit für die Zielregionen evaluiert und ihre Kombinationsfähigkeit mit dem entgegengesetzten heterotischen Gen-Pool in Testkreuzungen mit einer Einfachkreuzung als Tester bewertet. (ii) Für eine geringe Zahl (< 6) von Landrassen wird anschließend eine große Anzahl von DH-Linien erstellt, welche für die Nutzung in der Assoziationskartierung und/oder genomischen Selektion phänotypisiert und genotypisiert werden, um diese „Goldreserven“ für die Maiszüchtung mit innovativen Methoden zugänglich zu machen.