Browsing by Person "Geiger, Hartwig H."

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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.
Entwicklung, Charakterisierung und Kartierung von Mikrosatellitenmarkern bei der Zuckerrübe (Beta vulgaris L.)
(2001) Dörnte, Jost; Geiger, Hartwig H.
Simple sequence repeats (SSRs) or microsatellites were isolated from a sugarbeet (Beta vulgaris L.) genomic phage library. The size-fractionated library was screened for the occurrence of the motifes (GA)n, (GT)n, (TGA)n, (AGA)n and (CCG)n. The motifes (GA)n and (GT)n were found to occur most frequently in the sugarbeet genome (every 225 kb). In contrast, the trimer motifes were half as frequent (every 527 kb). A total of 217 microsatellite sequences were found in the sequenced clones. Most of the repeats were imperfect and/or compound. Sequence comparison revealed that 23% of the clones wich containing the (GT)n motif are variants of a previously described satellite DNA (SCHMIDT et al. 1991). Of 102 primer pairs tested on sugarbeet DNA, 71 gave a single product in the expected size. On 23 sugarbeet samples 64 of the 71 SSR-markers reveald length polymorphisms. The number of detected alleles per marker ranged from 2 to 13 (average 4,9) and the PIC-values ranged from 0,17 to 0,86 (average 0,58). A cluster analysis of the 23 samples confirms the pedigree data. The developed SSR markers were compared with RFLP and AFLP markers. Therefore nine sugarbeet lines, each with five single plants per line, were analysed. The SSR analyse shows the lowest similarity between the nine lines. The similarity inside the lines revealed no differences between the marker assays. Thirtythree SSR markers were genetically mapped into the RFLP framework maps of 2 F2-populations. The markers are randomly distributed over eight linkage groups of sugar beet.
Experimental and simulation studies on introgressing genomic segments from exotic into elite germplasm of rye (Secale cereale L.) by marker-assisted backcrossing
(2005) Susic, Zoran; Geiger, Hartwig H.
The introgression of exotic germplasm is a promising approach to increase the genetic diversity of elite rye breeding materials. Even though exotic germplasm may contain genomic segments that can improve oligo- and polygenically inherited traits, it has not been intensively utilized in modern rye breeding due to its agronomically inferior phenotypes and low performance level. Introgression of exotic germplasm requires techniques that would minimize negative side effects attributable to genetic interactions between recipient and donor. This appears achievable by the introgression library approach involving the systematic transfer of donor chromosome (DC) segments from an agriculturally unadapted source (donor) into an elite line (recipient, recurrent parent). A set of introgression lines (ILs) is thus developed, in which introgression is restricted to one or a few short DC segments. Ideally, the introgressed DC segments are evenly distributed over the whole recipient genome and the total genome of the exotic donor is comprised in the established set of ILs. The systematic development of an introgression library in rye has not been described yet. The main objectives of this study were to i) establish two rye introgression libraries by marker-assisted backcrossing, comprising of ILs each harbouring one to three DC segments and jointly covering most of the donor genome (DG), and ii) apply computer simulations to develop a highly effective and cost-efficient marker-assisted introgression strategy for the creation of introgression libraries in rye. A cross between a homozygous elite rye inbred line L2053-N (recurrent parent) and a heterozygous Iranian primitive rye population Altevogt 14160 (donor) was used as base material to generate the two libraries (F and G). Repeated backcrossing (BC) and subsequent selfing (S) until generation BC2S3 were chosen as the introgression method. The AFLP and SSR markers were employed to select individuals carrying desired DC segments, starting from generation BC1 to generation BC2S2. The chromosomal localization of DC segments, the number of DC segments per IL, and the proportion of recurrent parent genome were used as criteria to select parent individuals. This procedure resulted in the first two rye introgression libraries worldwide, comprising 40 BC2S3 ILs per library and covering 72% of the total DG in library F and 63% in library G (jointly approximately 80%). Most of the established ILs harboured one to three homozygous DC segments (on average 2.2 in both libraries), with a mean length of 18.3 cM in library F and 14.3 cM in library G. Computer simulations were conducted using the software PLABSIM version 2 to evaluate and optimize strategies for developing an introgression library in rye. Simulations were based on map-length estimates obtained from genotyping the BC1 generation of population F (7 chromosome pairs, genome size 665 cM). Six strategies differing in the number of BC and S generations were analysed, by setting the restrictions of sufficient DG coverage and RPG recovery. The medium-long BC3S1 strategy proved to be the most recommendable. It allows to achieve close to 100% DG coverage with moderate progeny sizes (19 individual per IL) in the individual generations and an acceptable total number of marker data points (52700), thus providing a good compromise between the cost and speed of an introgression procedure. Longer strategies are somewhat more cost-efficient but too time-demanding. The reverse is true for shorter strategies. An optimal allocation of resources is achieved by starting an introgression strategy with a small BC1 population (between 60 and 200 individuals) and stepwise increasing the progeny size per IL from about 15 to about 25-35 individuals in the succeeding generations. Targeting longer DC segments and using genetic maps with lower marker density allow a remarkable reduction in resources. This approach, however, possesses shortcomings when implementation in breeding is considered. The longer DC segments more likely carry i) unfavourable loci as well, ii) more than one gene controlling the trait in question, or iii) many additional loci affecting other traits. The major disadvantage of genetic maps with large marker distances is the unknown information about possible double cross-overs within marker intervals. All above-mentioned disadvantages may cause problems in the process of identification and isolation of genes controlling the trait of interest. Thus, a lower initial effort for the establishment of an introgression library will later on require additional efforts for using the ILs in breeding and genomics. Since the results of the simulation study became available after the marker-assisted establishment of the two rye introgression libraries had been finished, the dimensioning of the experimental study deviated from the optimum dimensioning determined in the simulation study: i) The BC2S2 introgression strategy was used in the empirical approach, whereas the BC3S1 strategy proved to be most recommendable in the simulation study. ii) The BC1 population sizes of libraries F and G (68 and 69, respectively) were far below the optimum value (200) determined in the simulation study for the chosen BC2S2 strategy. iii) The mean progeny sizes per IL from generation BC2 onwards varied between 7 and 21, whereas the optimum progeny size would have been two to three times higher. iv) The total number of analysed individuals (690 in library F, 684 in library G) was considerably lower than the optimum determined in the simulation study (3440). As a consequence, the coverage of the donor genome in the two libraries was incomplete and most ILs harboured more than a single DC segment. The potential application of the results of the simulation study would have increased the value of the developed ILs (higher DG coverage, lower number of DC segments per IL) considerably, despite limited resources. The effects of the introgressed DC segments on agronomically important qualitative and quantitative traits still need to be examined in multi-environmental field experiments. Introgression lines with beneficial DC segments may directly be used in practical hybrid rye breeding programs. Moreover, such ILs may be further backcrossed to create near isogenic lines (NILs) each carrying a single marker-characterized short DC segment. These NILs are an ideal starting point for high-resolution mapping and for the isolation and functional characterisation of candidate genes. The two rye introgression libraries and the results of the simulation study mark important milestones for the targeted exploitation of exotic rye germplasm and provide a promising opportunity to proceed towards functional genomics in rye.
Genetische und physiologische Einflußfaktoren sowie deren Wechselwirkungen auf die Trichothecenbildung bei Roggen, Triticale und Weizen nach Inokulation mit Fusarium culmorum (W. G. Sm.) Sacc.
(2002) Reinbrecht, Carsten; Geiger, Hartwig H.
Fusarium culmorum causes specific hazards of cereal quality by the producion of trichothecenes. Prophylaxis by plant breeding can be highly effective. The aim of this study was to investigate the accumulation of trichothecenes in cereals with regard to host and fungal genotype, to physiological factors and the resulting interactions. To determine the effects of 6 environments (E), 2 inoculation dates (ID), 2 fungal isolates (I), and 5 conidia concentrations (C) and their interactions, field trials with up to 12 rye, 6 triticale, and 8 wheat genotypes (G) were conducted in 1995-1997. Kinetics of trichothecene in the heads were described with 6 harvest dates (H) in 2 host genotypes each. In a growth chamber, 2 levels of temperature (T) and 2 of relative humidity (R) were investigated by using 2 host genotypes each. Average deoxynivalenol (DON) accumulation of rye, triticale, and wheat was 41, 46, and 82 mg kg-1, respectively. Genotypes differed significantly in rye and wheat. In all cereal species, GxE interactions were important. In wheat, DON content was highly correlated to all resistance traits, whereas in rye only a tight correlation existed to the relative specific grain weight. In triticale and wheat, inoculation at full anthesis resulted in higher DON contents than inoculation at heading. In rye, no effect of inoculation date was found. In contrast, GxID interaction was significant in rye. The nivalenol (NIV) producing isolate led to lower trichothecene contents than the DON producing isolate. This effect was found to be significant only in rye and triticale. Significant GxI interactions occurred in wheat only. Even one week after inoculation, considerable DON concentrations could be obtained in harvested heads, especially in wheat. Maximum DON contents were observed between 3 and 6 weeks after inoculation (in wheat: partially above 300 mg kg-1). NIV contents were always lower than DON contents. Until full ripening, DON contents slightly decreased, whereas NIV contents increased continuously. HxE and HxI interactions were most important. Trichothecene content in chaff and spindles was 2-4 fold higher than in the respective kernels at 6 and 8 weeks after inoculation. With higher conidia concentrations, increasing contents of DON+3-Acetyl-DON were measured. GxC interactions were highly significant. Highest heritabilities were found in the upper concentration levels. When the relative humidity was high, trichothecene concentrations of kernels were superior. With the temperature, an inverse effect was obtained. It seems that GxT interaction contributed most to GxE in rye and wheat, in triticale also the GxR interaction. In conclusion, assisting resistance traits may replace an expensive quantification of trichothecenes in early generations. In advanced generations, tests should be conducted in several environments with high conidia concentrations, and a toxin analysis should be carried out directly.
Markergestützte Vererbungsanalyse der Pollenfertilitätsrestauration bei Winterroggen (Secale cereale L.)
(2001) Wolf, Markus; Geiger, Hartwig H.
In rye (Secale cereale L.) as in a number of other crossfertilized crops, hybrid breeding allows a targeted use of heterosis for improving yield and yield stability. The creation of hybrids in outbred rye requires an efficient system of pollination control because of the monoclinous inflorescence. In commercial seed production, mostly the Pampa (P-) Cytoplasma is used, which induces cytoplasmatic male sterility (CMS). Restoration of pollen fertility is achieved by means of pollinator lines carrying nuclear dominant restorer genes. To obtain information about the number, localization, and efficacy of the restorer genes, molecular marker based inheritance analysis in rye was performed. The results were compared to already localized restorer sources in rye and other species. Ninety-two marker loci were mapped by RFLP technique, which covered a genome-length of 845 cM. QTL (quantitative trait loci) analysis revealed a major gene on the short arm of chromosome 1R. Two RFLP markers, psr596 and bcd1124, were linked with a distance of about 0.3 cM to this major gene. Moreover, two modifying minor genes on chromosome arms 3RL and 5RL were detected. One of these minor genes showed epistatic interaction with the above mentioned major gene.
Optimizing the development of seed-parent lines in hybrid rye breeding
(2001) Tomerius, Alexandra-Maria; Geiger, Hartwig H.
In hybrid rye breeding, seed-parent and pollinator lines are developed from two divergent gene pools. Line development comprises selection for line performance per se followed by selection for combining ability to the opposite gene pool. Cytoplasmic-genic male sterility (CMS) is employed as hybridizing mechanism. This study deals with model calculations aiming to optimize and compare alternative schemes of seed-parent line development in hybrid rye breeding on the basis of their expected selection gain per year in an index comprising the most important breeding objectives. Prediction of selection gains rests on current estimates of quantitative-genetic and economic parameters. The schemes are optimized for the number of candidates, testers to assess testcross performance, test locations, and replicates at the individual selection stages. Optimization is carried out assuming a fixed annual budget. Five schemes are investigated which differ in the basic genetic material assumed, in the type of test units and the number of selection stages for line and testcross selection, and in the length. The standard scheme employs second cycle material. First, S2-lines are evaluated per se. Selection for combining ability is then carried out at two stages employing testcross progenies of the CMS analogues of the candidate lines in backcross generations BC1 resp. BC2. The first alternative scheme employs an additional stage of BC1L-testcross selection. Another scheme is suited for developing seed-parent lines from broader-based population material. In addition to these 'conventional' methods, a scheme using doubled haploid lines is investigated as well as a scheme in which testcross progenies are produced by means of a gametocide instead of CMS. The optimum dimensioning and relative efficiency of the schemes is investigated for various genetical and economical situations.
Recurrent selection for increased outcrossing rates of barley from semi-arid regions of Syria and Jordan
(2010) Nandety, Aruna; Geiger, Hartwig H.
Improving the grain yield in drought stress environments such as the semi-arid areas of the West Asia North Africa (WANA) region has been a persistent problem since many years. Although barley (Hordeum vulgare L.) is widely grown in this region, the possibility of a crop failure is high. Being an autogamous crop, barley cultivars display almost complete homozygosity. Population genetic studies have shown that heterozygous barley genotypes possess a significantly increased stress tolerance, thus, being superior in both the level and stability of yielding performance. Therefore, increasing the level of heterozygosity in barley was the general aim of this study. For this purpose, a new marker-assisted recurrent selection (RS) approach was developed and applied to a genetically broad based world collection of barley germplasm. The specific objectives of this study were: (1) to investigate the efficacy of the above approach, (2) to determine the gain in heterozygosity over four RS cycles and to evaluate the selection results in a final experiment under common environmental conditions, (3) to estimate the selection differential, response to selection and realized heritability and (4) to provide barley materials with increased heterozygosity to plant breeding programs in the WANA region. Applying the RS approach, only plants showing superior levels of heterozygosity at co-dominant molecular marker (SSR) loci were advanced to successive selection cycles. These heterozygous plants were expected to carry a combination of advantageous alleles a) for open flowering from the female parent, and b) for pollen shedding from the male parent. For marker assessment, bulking of the plants and multiplexing of the SSR markers was practised in each selection cycle to save time and labour. The most polymorphic bulks were genotyped plant-wise and seed of the most heterozygous plants was advanced to the subsequent RS cycles. In the course of the RS experiment, a base population was compiled from 201 gene bank accessions held by the ?International Center for Agricultural Research in Dry Areas? (ICARDA) and the ?Institute of Plant Genetics and Crop Plant Research? (IPK) in Germany. Selection led to a stepwise increase in the heterozygosity from 0.60% in the base population to 3.24% after four cycles of selection. In the base population, the six-rowed landraces showed higher heterozygosity than the two-rowed. Selection response was highest in the first RS cycle which may be attributable to a major decline of the genetic variance from cycle to cycle and to a severe reduction of the population size due to strong dormancy among the entries selected in the first RS cycle. Very low realized heritabilities for observed heterozygosity were obtained in each RS cycle. Nevertheless, significant selection response was obtained. In order to compare the results of the individual RS cycles under common environmental conditions, preserved seed from each of the selected parent plants was grown in a final greenhouse experiment. Beside heterozygosity, various development, flowering and performance traits (days to ear emergence, anther extrusion, open flowering, number of ear bearing tillers, 100-grain weight and seed number) were additionally assessed in this experiment. The observed heterozygosity increased from 0.23% in population C1 via 0.69% in C2 and C3 to 1.29% in C4. The marker genotypes assessed in the final experiment were used to estimate multi-locus outcrossing rates. Values increased from 1.4% in C1 via 2.1% in C2 to 2.8% in C3 and C4. Generally, the increase from cycle to cycle was significant. Only the progress from C1 to C2 and from C3 to C4 did not reach the 5% significance level. All estimates were probably downward biased due to extremely high temperatures in the greenhouse during flowering. Great differences existed between the outcrossing rates of individual families within populations. Only non-significant weak to negligible correlations were obtained between floral traits and the outcrossing rate. The observed positive response to recurrent selection substantiates the efficacy of the present approach for enhancing the level of heterozygosity in barley, offering good perspectives for improving the productivity of the crop in the stress prone WANA region. The new selection approach, in principle, is applicable to other autogamous or partially autogamous crop plants as well.
Untersuchungen zur Bedeutung der Stickstoffeffizienz für die Ertragssicherheit bei Mais
(2002) Thiemt, Elisabeth-M.; Geiger, Hartwig H.
Increased fertilization with nitrogen (N) in maize production areas often leads to pollution. Maize varieties with improved N-use efficiency under low soil N conditions can therefore contribute to sustainable agriculture. The objectives of this study were to investigate, whether i) hybrids with special adaptation to low soil nitrogen condition show higher yield stability than those which were selected in high nitrogen environments , ii) N-efficient hybrids are more tolerant to drought conditions, iii) combination of parent lines with differences in N-efficiency leads to increased heterosis , and iiii) hybrids show differences concerning components of N-efficiency, in particular N-uptake and N-utilization efficiency. A set of hybrids was generated with parent lines showing superior testcross performance at low or high N-levels, designated L-lines and H-lines, respectively. Field trials were conducted in 14 environments: each trial was grown under high (NH) and low (NL) nitrogen level. Under NL-conditions LxL-hybrids outyielded HxH-hybrids significantly, while at NH the HxH-hybrids showed higher grain yield than LxL hybrids. N-efficient hybrids did not show increased drought tolerance. LxL-hybrids tended to have higher yield stability than HxH-hybrids. Significant increase of heterosis for the traits dry matter yield and dry matter content was not found, neither at NL nor at NH-level. Under NL-conditions N-uptake was reduced, but N-utilization efficiency increased.
Untersuchungen zur Vererbung von Qualitätseigenschaften bei Silomais (Zea mays L.)
(2004) Krützfeldt, Birte A. E.; Geiger, Hartwig H.
In central Europe silage maize (Zea mays L.) is a major source of cattle feed. The quality or the feeding value of a silage maize variety mainly depends on its digestibility and energy content. The establishing of the near-infrared-reflectance-spectroscopy- (NIRS) technique allows the analysis of more than one quality determining trait simultaneously in an easy and short way. In this study one objective was the influence of stover quality on whole plant quality. In hybrid breeding indirect selection on the basis of inbred line performance has a great advantage because the number of testcrosses can be reduced. Therefore it was tested, if the stover quality of the testcrosses could be predicted on the line per se value. Besides the correlation between agronomic and quality traits was analysed. In the years 1999 and 2000 the evaluation of the stover of the lines and testcrosses and the whole plant of the testcrosses was conducted at four climatically diverse sites in Germany. Three data sets with flint-lines and dent-lines, each proved with one tester-line, were evaluated for the correlation between inbred line and testcross performance. The test for combining ability was performed with three smaller data sets also consisting of flint-lines and dent-lines with two tester-lines per data set. The coefficients of heritability were high for the agronomic and quality traits in the data sets of the inbred lines. In the data sets of the testcrosses the variation attributed to the genotypic variance was smaller, genotype × location-interactions were of lower importance. In the data sets, each with two tester-lines it was obvious that for quality traits of stover and whole plant the interaction between line and tester was mostly not significant. The genotypic correlation between inbred line and testcross performance was highly significant for almost all quality traits of the stover, but the correlation coefficients were mostly only moderate. Only the expected success of an indirect selection on line per se- value for cell-wall digestibility of the stover exceeded that of the direct selection on testcross performance in all data sets. However, a selection of extremes on line per se value should be possible for stover digestibility. The genotypic correlations between comparable traits in stover and whole plant were mainly low. The cell-wall digestibility was the only trait which was independent of dry matter content. For evaluation of the further quality traits attention has to be paid to the maturity stage, to prevent a maturity-based bias of the results. In the testcrosses stover digestibility increased and whole plant digestibility was reduced with an increase in whole plant dry matter yield. But the genotypic correlations were only moderate and a simultaneous selection to improve quality and yield seems to be possible.