Browsing by Subject "Roggen"

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Analyzing resistance to ergot caused by Claviceps purpurea [Fr.] Tul. and alkaloid contamination in winter rye (Secale cereale L.)
(2022) Kodisch, Anna; Miedaner, Thomas
Ergot caused by Claviceps purpurea [Fr.] Tul. is one of the oldest well-known plant diseases leading already in medieval times to severe epidemic outbreaks. After the occurrence of honeydew, the characteristic ergot bodies called sclerotia are formed on the ear. These are containing toxic ergot alkaloids (EAs). Strict limits are set within the European Union. Rye (Secale cereale L.) as cross-pollinating crop is particularly vulnerable to ergot since the competitive situation of fungal spores and pollen during flowering. Nevertheless, even today the threat is real as agricultural practice is changing and screening studies revealed EAs in samples of the whole cereal value chain frequently. The aims were to establish a harmonized method to test ergot resistance and EA contamination in winter rye, to clarify major significant factors and their relevance and to reveal the suitability of one commercial ELISA test. Further, effort was paid to examine the covariation of ergot amount and EA content considering different factors because of prospective legislative changes. Genotypes showed significant variation for ergot severity and pollen-fertility restoration after natural infection as well as artificial inoculation whereas a high positive correlation could be found between both treatments. Additionally, variances of environment, general combining ability (GCA), specific combining ability (SCA), and interactions were significant. Although male pollen-fertility restoration was of utmost importance, the female component was also significant. This illustrates that apart from promising selection of high restoration ability the maternal restorability could be exploited in future breeding programs especially when a high pollen amount is already reached. A large-scale calibration study was performed to clarify the covariation of ergot severity, EA content (HPLC, ELISA) considering genotypes, locations, countries, years, and isolates. EA profile was rather stable across country-specific isolates although large differences regarding the EA content were detected. The moderate covariation between ergot severity and EA content (HPLC) indicates that a reliable prediction of the EA content based on ergot severity is not possible what can also not be explained by grouping effects of the factors. Further, EAs seem not to act as virulence factor in the infection process since EA content showed no relationship to disease severity. Additionally, the missing correlation of ELISA and HPLC leads to the conclusion that the ELISA is not an appropriate tool what can be used safely to screen samples regarding ergot in the daily life. The genetic variation of male-sterile CMS-single crosses was analysed in a special design without pollen in field and greenhouse to identify resistance mechanisms and to clarify whether ergot can be reduced in the female flower. At this, comparison of needle and spray inoculation revealed medium to high correlations illustrating that both methods were suitable for this research. Significant environment and genotype by environment interaction variances were detected. So, testing across several environments is necessary also without pollen. Further, small but significant genotypic variation and identification of one more ergot-resilient candidate revealed that selection of female lines could be promising to further reduce ergot. The EA content was lower for less susceptible genotypes. Thus, EA content can be considerably reduced by breeding. A strong positive correlation could be found for ergot severity and EA content when analysing 15 factorial single crosses. The male pollen-fertility restoration was also here the most relevant component but the female component contributed an obviously higher proportion for the EA content than for ergot severity. In conclusion, this thesis demonstrate that implementing of a high and environmental stable male fertility restoration ability via exotic Rf genes can effectively reduce ergot although also the female restorability enables great opportunities. The unpredictable covariation between ergot amount and EA content illustrates that both traits have to be assessed, in particular the EA content by a valid HPLC approach to guarantee food and feed safety.
Effects of seed coating on germination and early seedling growth in cereals
(2014) Gorim, Linda Yuya; Asch, Folkard
Grain cereals such as barley, rye, wheat or sorghum, constitute a major share in human diet worldwide. Climate change threatens cereal production systems due to emerging unreliable rainfall patterns and thus, renders crop production vulnerable to early season failure of crop establishment. Breeding drought tolerant genotypes is a long and complicated process, thus not suited to respond to environmental changes quickly but rather to address the problem in a longer time frame. Seed coats increasing water availability to the seed and enhancing early vigor of the seedling may be a better short term solution. Seed coats containing hydro-absorbers such as Stockosorb® or Geohumus® can improve water availability and in combination with other substances for example humic acids or plant fortifiers such as Biplantol® may improve early vigor. However, very low germination rates have been observed in seeds coated in this way resulting in slow adoption of seed coating technology in agriculture. The present study analyzed the effects of seed coating on germination, which seed coat composition can enhance germination rate and early vigor and why, the effects of seed coat on germination and seed physiology, and which influence seed coats containing different kinds of hydro-absorbers have on the drought resistance of seed during germination. Studies were conducted on barley, rye, and wheat seeds. In these species the mode of action of differently composed seed coats and the effects of differences in seed coat strength were studied whereas the studies on drought resistance were performed with sorghum seeds. The following results were obtained and submitted for international publication: 1) Seed coating in general reduced germination rates as compared to uncoated seeds. Seed coating thickness was the determining factor. With a share of the seed coat of 75% of the total grain (seed + seed coat) germination was very little affected by coating. However, smaller seed coat shares and particularly shares smaller than 50% of the total grain severely reduced germination rate. This effect was especially pronounced in wheat. 2) With seed coat shares larger than 75% and the coats dotted with different substances generally resulted in high germination rates. However, strong genotypic effects were observed in responses of seed physiology and dry matter partitioning to the different substances included in the coat, with barley generally responding positively, rye intermediate and in wheat generally the weakest effects were observed. Across genotypes Biplantol included in the coat mainly promoted shoot growth, humic acid increased root growth and hydro-absorbers mainly the rate of germination and early vigour. Due to those results only seed coated with hydro-absorber containing coat and with coat not smaller than 75% were used for all following studies. 3) Seedlings growing from coated seeds with coat shares > 75% showed accelerated early seedling growth with strongly reduced respiratory losses during the mobilization of endosperm reserves, combined with significantly increased mobilisation efficiency in all three cereals. Analyses showed that the sucrose metabolism and thus the availability of glucose as energy provider for growth differed strongly between coated and uncoated seeds as well as among the cereal species. Embryos from coated seed (particularly in barley and wheat) seemed to grow better with significantly less glucose indicating a chance in the enzymatic cleavage of sucrose that could only be due to the higher energy efficiency of the enzyme sucrose synthase. 4) Studies during germination in sensu stricto (the first 48h hours after soaking) showed that in the embryos of coated seeds conditions were hypoxic with oxygen concentrations of less than 5% of atmospheric oxygen as compared to 60-80% oxygen of atmosphere in embryos of uncoated seeds. From this it was deduced that the lower respiratory losses during germination of coated seeds are due to a switch in sugar metabolism from invertase based cleavage of sucrose to sucrose synthase based cleavage of sucrose which is the less energy demanding pathway in the near absence of oxygen. 5) A last study on drought resistance of coated seed whose coats comprised two different hydro-absorbers (Stockosorb or Geohumus) showed that the drought responses of coated seed differed little form uncoated seeds. However, seedling growth under both drought and fully watered conditions was affected by the type of hydro-absorber in the coat. Whereas Stockosorb promoted rather root growth,Geohumus enhanced shoot growth. In conclusion, it can be stated that seed coats investigated in this study in general promoted germination rate and success in cereals if the seed coat has the appropriate strength i.e. coat shares not below 75% of total grain. Additives such as Biplantol or humic acid promote vigour and influence dry matter partitioning in favour of specific organs which could be employed as management options during germination. It was shown that seed coats influence the germination and seedling metabolism und induce hypoxic conditions in embryonic tissue which shift the sugar metabolism to a more energy efficient pathway. Oxygen dynamics in the different seed tissues require further studies and need to be better understood in order to employ the positive effects of seed coating in a targeted and species-specific approach to improve and enhance crop establishment particularly in drought prone cereal production systems. Another future pathway could be including nutrients in the coat that promote early seedling growth and for systems threatened by early drought spells or unreliable rainfall a seed coat that would conduct water to the seed only after soil moisture has surpassed a given threshold and thus induces germination only when water availability is optimal.
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.
Genetische Variation für Resistenz gegen Mutterkorn (Claviceps purpurea [Fr.] Tul.) bei selbstinkompatiblen und selbstfertilen Roggenpopulationen
(2006) Mirdita, Vilson; Miedaner, Thomas
Ergot (Claviceps purpurea [Fr.] Tul.) is one of the most important diseases in rye. Infection during flowering results in the production of black, overwintering organs (sclerotia) instead of kernels, which contain harmful alcaloids. Three experiments were conducted to estimate quantitative-genetic parameters of the resistance of rye to ergot under the conditions of organic farming. The general aim was the estimation of genetic variation among and within self-incompatible rye populations and among CMS lines and their male-sterile testcrosses. In 2002 and 2004, genetic variation in resistance to ergot was tested among 65 rye populations at each of two locations (Experiment 1). Thirteen populations were registered rye varieties and the remaining 52 were genetic resources. To assess genetic variation within populations, 50 full-sib families (FSF) from each of five rye populations were developed and tested at four locations (Experiment 2). To test genetic differences in the susceptibility of ovaries towards fungal penetration in the absence of pollen, (i) 64 currently available CMS lines and (ii) their male-sterile crosses with three testers (=sets) were tested in 2003 and 2004, and in 2004, respectively. Inoculation was performed by spraying an aggressive mixture of isolates of Claviceps purpurea three times during the flowering period. The micro-plots were grown in a chess-board design separated by wheat plots to reduce the neighbouring effects. Traits of resistance were the proportion of infected spikes relative to the total number of spikes per plot, and the percentage by weight of ergot sclerotia in the grain. In Experiment 3, the weight of slcerotia per spike and per pair of spikelet were measured due to the absence of grain. Amount of pollen shedding was rated on the basis of the anther size and extrusion. Highly significant genotypic and genotype-environment interaction variances were found among rye populations in the percentage of ergot sclerotia in the grain. All genotypes were infected by ergot. No differences in mean among the registered rye varieties and genetic resources were detected. Because all populations were highly pollen shedding, the results indicate the existence of genetically determined resistance to ergot within the self-incompatible rye. Correlation between both resistance traits was significant (rp = 0.92). Genetic variation within populations was highly significant for all five populations. Individual progenies with resistance higher than the population mean were observed. The mean resistance of initial populations hardly differed from the mean of their progeny indicating a predominantly additive inheritance. Highly significant genetic variation in resistance to ergot was also detected among the currently available 64 CMS lines. Corresponding testcrosses mostly had a higher weight of sclerotia per spike than the lines. Considerable differences in the level of resistance were observed among testcrosses. Crosses with tester line 1 were substantially more susceptible, whereas those with tester 2 were hardly over the mean of the parental lines. The material showed a quantitative distribution of ergot resistance. Weak to medium-sized correlations (0.33 ? 0.47) between locations were detected among lines. The correlation between locations was even weaker in testcrosses. Weak correlations in ergot weight per spike were observed between CMS lines and their testcrosses in sets 2 and 3. In set 1, the estimated phenotypic correlation was higher (rp = 0.65). Estimates of error-corrected correlations were always higher than phenotypic correlations. No genetic difference was detected among the CMS lines for the amount of alkaloids in their sclerotia. This study shows that incompatible rye populations as well as self-fertile hybrid populations contain a substantial genetic variation for resistance to ergot that is inherited quantitatively. In both materials, mainly additive genetic variance was found. Because of a significant genotype-environment interaction, multi-environment trials are necessary to select for resistance. The results of this study nevertheless indicate good prospects to improve resistance to ergot in rye breeding in the long term.
Genomic prediction in rye
(2017) Bernal-Vasquez, Angela-Maria; Piepho, Hans-Peter
Technical progress in the genomic field is accelerating developments in plant and animal breeding programs. The access to high-dimensional molecular data has facilitated acquisition of knowledge of genome sequences in many economically important species, which can be used routinely to predict genetic merit. Genomic prediction (GP) has emerged as an approach that allows predicting the genomic estimated breeding value (GEBV) of an unphenotyped individual based on its marker profile. The approach can considerably increase the genetic gain per unit time, as not all individuals need to be phenotyped. Accuracy of the predictions are influenced by several factors and require proper statistical models able to overcome the problem of having more predictor variables than observations. Plant breeding programs run for several years and genotypes are evaluated in multi environment trials. Selection decisions are based on the mean performance of genotypes across locations and later on, across years. Under this conditions, linear mixed models offer a suitable and flexible framework to undertake the phenotypic and genomic prediction analyses using a stage-wise approach, allowing refinement of each particular stage. In this work, an evaluation and comparison of outlier detection methods, phenotypic analyses and GP models were considered. In particular, it was studied whether at the plot level, identification and removal of possible outlying observations has an impact on the predictive ability. Further, if an enhancement of phenotypic models by spatial trends leads to improvement of GP accuracy, and finally, whether the use of the kinship matrix can enhance the dissection of GEBVs from genotype-by-year (GY) interaction effects. Here, the methods related to the mentioned objectives are compared using experimental datasets from a rye hybrid breeding program. Outlier detection methods widely used in many German plant breeding companies were assessed in terms of control of the family-wise error rate and their merits evaluated in a GP framework (Chapter 2). The benefit of implementation of the methods based on a robust scale estimate was that in routine analysis, such procedures reliably identified spurious data. This outlier detection approach per trial at the plot level is conservative and ensures that adjusted genotype means are not severely biased due to outlying observations. Whenever it is possible, breeders should manually flag suspicious observations based on subject-matter knowledge. Further, removing the flagged outliers identified by the recommendedmethods did not reduce predictive abilities estimated by cross validation (GP-CV) using data of a complete breeding cycle. A crucial step towards an accurate calibration of the genomic prediction procedure is the identification of phenotypic models capable of producing accurate adjusted genotype mean estimates across locations and years. Using a two-year dataset connected through a single check, a three-stage GP approach was implemented (Chapter 3). In the first stage, spatial and non-spatial models were fitted per locations and years to obtain adjusted genotype-tester means. In the second stage, adjusted genotype means were obtained per year, and in the third stage, GP models were evaluated. Akaike information criterion (AIC) and predictive abilities estimated from GP-CV were used as model selection criteria in the first and in the third stage. These criteria were used in the first stage, because a choice had to be made between the spatial and non-spatial models and in the third stage, because the predictive abilities allow a comparison of the results of the complete analysis obtained by the alternative stage-wise approaches presented in this thesis. The second stage was a transitional stage where no model selection was needed for a given method of stage-wise analysis. The predictive abilities displayed a different ranking pattern for the models than the AIC, but both approaches pointed to the same best models. The highest predictive abilities obtained for the GP-CV at the last stage did not coincide with the models that AIC and predictive ability of GP-CV selected in the first stage. Nonetheless, GP-CV can be used to further support model selection decisions that are usually based only upon AIC. There was a trend of models accounting for row and column variation to have better accuracies than the counterpart model without row and column effects, thus suggesting that row-column designs may be a potential option to set up breeding trials. While bulking multi-year data allows increasing the training set size and covering a wider genetic background, it remains a challenge to separate GEBVs from GY effects, when there are no common genotypes across years, i.e., years are poorly connected or totally disconnected. First, an approach considering the two-year dataset connected through a single check, adjusted genotype means were computed per year and submitted to the GP stage (Chapter 3). The year adjustment was done in the GP model by assuming that the mean across genotypes in a given year is a good estimate of the year effect. This assumption is valid because the genotypes evaluated in a year are a sample of the population. Results indicated that this approach is more realistic than relying on the adjustment of a single check. A further approach entailed the use of kinship to dissect GY effects from GEBVs (Chapter 4). It was not obvious which method best models the GY effect, thus several approaches were compared and evaluated in terms of predictive abilities in forward validation (GP-FV) scenarios. It was found that for training sets formed by several disconnected years’ data, the use of kinship to model GY effects was crucial. In training sets where two or three complete cycles were available (i.e. there were some common genotypes across years within a cycle), using kinship or not yielded similar predictive abilities. It was further shown that predictive abilities are higher for scenarios with high relatedness degree between training and validation sets, and that predicting a selection of top-yielding genotypes was more accurate than predicting the complete validation set when kinship was used to model GY effects. In conclusion, stage-wise analysis is recommended and it is stressed that the careful choice of phenotypic and genomic prediction models should be made case by case based on subject matter knowledge and specificities of the data. The analyses presented in this thesis provide general guidelines for breeders to develop phenotypic models integrated with GP. The methods and models described are flexible and allow extensions that can be easily implemented in routine applications.
Integration of hyperspectral, genomic, and agronomic data for early prediction of biomass yield in hybrid rye (Secale cereale L.)
(2021) Galán, Rodrigo José; Miedaner, Thomas
Currently, the combination of a growing bioenergy demand and the need to diversify the dominant cultivation of energy maize opens a highly attractive scenario for alternative biomass crops. Rye (Secale cereale L.) stands out for its vigorous growth and increased tolerance to abiotic and biotic stressors. In Germany, less than a quarter of the total harvest is used for food production. Consequently, rye arises as a source of renewables with a reduced bioenergy-food tradeoff, emerging biomass as a new breeding objective. However, rye breeding is mainly driven by grain yield while biomass is destructively evaluated in later selection stages by expensive and time-consuming methods. The overall motivation of this research was to investigate the prospects of combining hyperspectral, genomic, and agronomic data for unlocking the potential of hybrid rye as a dual-purpose crop to meet the increasing demand for renewable sources of energy affordably. A specific aim was to predict the biomass yield as precisely as possible at an early selection stage. For this, a panel of 404 elite rye lines was genotyped and evaluated as testcrosses for grain yield and a subset of 274 genotypes additionally for biomass. Field trials were conducted at four locations in Germany in two years (eight environments). Hyperspectral fingerprints consisted of 400 discrete narrow bands (from 410 to 993 nm) and were collected in two points of time after heading for all hybrids in each site by an uncrewed aerial vehicle. In a first study, population parameters were estimated for different agronomic traits and a total of 23 vegetation indices. Dry matter yield showed significant genetic variation and was stronger correlated with plant height (r_g=0.86) than with grain yield (r_g=0.64) and individual vegetation indices (r_g: =<|0.35|). A multiple linear regression model based on plant height, grain yield, and a subset of vegetation indices surpassed the prediction ability for dry matter yield of models based only on agronomic traits by about 6 %. In a second study, whole-spectrum data was used to indirectly estimate dry matter yield. For this, single-kernel models based on hyperspectral reflectance-derived (HBLUP) and genomic (GBLUP) relationship matrices, a multi-kernel model combining both matrices, and a bivariate model fitted also with plant height as a secondary trait, were considered. HBLUP yielded superior predictive power than the models based on vegetation indices previously tested. The phenotypic correlations between individual wavelengths and dry matter yield were generally significant (p < 0.05) but low (r_p: =< |0.29|). Across environments and training set sizes, the bivariate model yielded the highest prediction abilities (0.56 – 0.75). All models profited from larger training populations. However, if larger training sets cannot be afforded, HBLUP emerged as a promising approach given its higher prediction power on reduced calibration populations compared to the well-established GBLUP. Before its incorporation into prediction models, filtering the hyperspectral data available by the least absolute shrinkage and selection operator (Lasso) was worthwhile to deal with data dimensionally. In a third study, the effects of trait heritability, as well as genetic and environmental relatedness on the prediction ability of GBLUP and HBLUP for biomass-related traits were compared. While the prediction ability of GBLUP (0.14 - 0.28) was largely affected by genetic relatedness and trait heritability, HBLUP was significantly more accurate (0.41 - 0.61) across weakly connected datasets. In this context, dry matter yield could be better predicted (up to 20 %) by a bivariate model. Nevertheless, due to environmental variances, genomic and reflectance-enabled predictions were strongly dependant on a sufficient environmental relationship between data used for model training and validation. In summary, to affordably breed rye as a double-purpose crop to meet the increasing bioenergy demands, the early prediction of biomass across selection cycles is crucial. Hyperspectral imaging has proven to be a suitable tool to select high-yielding biomass genotypes across weakly linked populations. Due to the synergetic effect of combining hyperspectral, genomic, and agronomic traits, higher prediction abilities can be obtained by integrating these data sources into bivariate models.
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.
Phenotypic and molecular analyses of grain and biomass productivity under irrigated and rainfed conditions in hybrid rye
(2014) Gottwald, Marlen; Miedaner, Thomas
Rye (Secale cereale L.) is a small grain cereal used for bread making, livestock feeding and as renewable energy source. These types of usages are leading to different breeding goals. Rye growing regions are affected by climate change and consequently by drought. Germany is touched by rainless periods in spring and early summer in the last years. Again, in spring 2012 farmers in Brandenburg and Lower Saxony were affected by drought periods. Yield losses in those regions, especially in combination with sandy soils are expected. Therefore much attention is paid for breeding of drought resistant germplasm. Briefly, our objectives of this study were to (1) estimate the biomass and biogas potential of different plant materials, their quantitative genetic parameters and biogas-related traits, (2) analyze two recombinant inbred lines and differences in their yield potential between irrigated and rainfed regime, as well as the relative efficiency for indirect selection for drought resistance in irrigated regime, and (3) investigate the phenotypic performance for ten agronomic and quality traits across multiple environments and estimated the number and effects underlying QTL. For the biomass-/ biogas analyses a wide range of plant material was analysed. Germplasm resources, full-sib families selected for grain and forage use were tested for their per se and testcross performance and experimental hybrids selected for grain use and population cultivars selected for grain and forage use were analyzed. Dry matter yields varying across environments from 106 to 177 dt/ha for per se and testcross performance, respectively. For testcross performance, germplasm resources showed similar values to forage rye. The later the maturity stage, the more dry matter yield on the whole plant level was achieved. Estimates of genotypic variances for biomass yield were significant for all rye materials, whereas the variances per se and for testcrosses were for germplasm resources exorbitant higher than for forage and grain rye. Typical cumulative methane production curves were obtained for the whole plant material from the Hohenheim biogas yield test. Methane yield showed large differences between second and third harvest date for individual plant fractions. Differences between genotypes were not substantial for methane yield although significant in some instances. At EC77/83 hybrids and forage rye reached similar methane yield of about 5000 m3/ha. A high correlation between dry matter yield and methane yield was observed (r=0.95). Concerning high cost and time consuming analysis of biogas tests, for breeders the main breeding goal should be maximum dry matter yield. Direct selection on dry matter yield should indirect improve methane yield. Two biparental populations were used for the analysis of drought tolerance. The analysis was performed in duplicate. Both populations were grown under irrigated and rainfed regimes. Striking less rainfall compared to long-term precipitation occurred between April and July, during critical phases of plant development. Grain yield reduction between irrigated and non-irrigated regime ranged from 2% to 29.6% for population A and 2% to 40% for population B, whereas differences between both regimes were significant (P<0.05) for five and four environments, respectively. Genotypic variances of grain yield were significant in all instances, whereas genotype by irrigation interaction variance between both regimes being significant only in three and four environments for population A and B, respectively. Analysis across those environments revealed significant difference for genotype by irrigation interaction variance and the three-way interaction variance in both populations. Heritability estimates were higher for the irrigated than for the rainfed regime. High interaction variance with environment and no clustering of the two regimes in a multi-dimensional analysis were found. This illustrates the different soil and whether conditions between locations and additionally every location suffered from a different drought stress. The correlation between both regimes was significant but moderate, but genotypic coefficients considerably higher (Pop-A: 0.86, Pop-B: 0.84), which could be substantiated that testcrosses differed not substantially in drought-resistance. Indirect selection for drought in the irrigated regime was predicted to be equally or more efficient than direct selection in the non-irrigated regime. Phenotypic and genotypic analysis was done across ten environments for both biparental populations for the general improvement of agronomic and quality traits in rye. Population A were genotyped with a Rye5K SNP array and for population B DArT genotyping was done with a 3K rye array. Additionally both populations were genotyped with about 150 SSRs. The genetic linkage maps comprised 1,819 and 1,265 markers for population A and B, respectively and were used for the QTL analysis for ten agronomic and quality traits. Phenotyping revealed large genetic variation for ten agronomic and quality traits. Intensive phenotyping at up to ten environments led to moderate to high heritabilities. Across environments explained genotypic variance of the individual QTL ranged from 5 to 55%. For 1000-kernel weight, test weight, falling number, and starch content, several QTL with high effects and a frequency of recovery of about 90% were identified in both population. Rye suffered from drought stress in the last decade. Focusing on general improvement of rye regarding yield and quality, as well as improving rye regarding drought-resistance is important. Future research should be done in fine mapping and validation of the detected QTLs, for exploiting their potential in marker assisted breeding.
Quantitative-trait loci (QTL) mapping of important agronomical traits of the grain and biomass production in winter rye (Secale cereale L.)
(2015) Haffke, Stefan; Miedaner, Thomas
Rye is an important crop in Northern and Eastern Europe and mainly used for food and feed and became most recently important for biogas production. Hybrid rye varieties dominate the cultivated area, which is mainly on light and sandy soils, because rye has a relatively high tolerance to biotic and abiotic stress factors. Climate change will also affect Central Europe, causing higher temperatures and less precipitation in spring and summer. Rye will be influenced more by these effects than other cereals because it is mainly grown on marginal environments. Rye has a high potential for being used as a biogas substrate, but detailed information on improving this trait in hybrid rye is missing. Until now, no study that analyzed phenotypic and genotypic agronomic traits for using rye for biogas production exists. Further, there is only one study, which dealt with the influence of periodic drought stress in rye cultivated areas. Beside this, we analyzed yield stability over a wide range of environments in consideration of drought stress in Central Europe. We analyzed an interpool hybrid population (Pop-D) in 2011 and 2012 at seven environments in Germany for the biomass yield and grain yield (Publication I). This study showed low correlations between grain yield and dry matter yield (r = 0.33). Higher correlations were obtained with two plant height measurements (at heading time, r = 0.64; before harvest, r = 0.52) and dry matter yield. The indirect selection via plant height was superior in contrast to the direct selection of dry matter yield by factor 1.24. Genotypic results confirmed phenotypic results as no overlapping QTL for grain yield and dry matter yield were detected (Publication II). However, we identified common gene regions for plant height and dry matter yield due to the high correlation between both. Plant height is a promising trait for indirectly selecting high biomass yielding varieties. The paradigm shift from shorter plants with high grain yield to taller hybrids as a resource for biogas substrate needs additional breeding efforts for lodging resistance. In Publication III we analyzed two intrapool populations (Pop-A and -B) and one interpool population (Pop-C) at 16 – 18 environments (location x year combinations) under irrigated and rainfed conditions in Germany and Poland. Yield stability was high over a wide range of environments, even when drought stress environments were included. This illustrates the adaption of rye to marginal and drought stress environments. The analyzed populations showed no differences within yield stability, but yield differences between inter- (Pop-C) and intra-pool (Pop-A and -B) crosses were visible. Selection for yield stability is possible due to the genetic variance for this trait within all three populations. Therefore, it is important to select genotypes with low genotype x environment interaction. All three populations showed high yield stability on a high yield level and were already well adapted to extreme weather events caused by climate change. It is recommended to use highly diverse environments with irrigated and rainfed conditions to select on yield stability and high yielding varieties under optimum and drought conditions
Ruminal degradation characteristics of barley, rye, and triticale grains assayed in situ and in vitro, and by near-infrared spectroscopy
(2017) Krieg, Jochen; Rodehutscord, Markus
The milk yield of dairy cows and related energy and protein requirements have steadily increased in the last few decades. Since feed intake has not increased to the same extent as nutritional requirements, the concentration of nutrients in mixed rations had to be increased. An increase in energy concentration is often achieved by the inclusion of high levels of cereal grains. In the EU—apart from wheat—barley, rye, and triticale are widely cultivated cereal grains. Starch (ST), followed by crude protein (CP), is the main constituent of cereal grains. The rate and extent of ruminal CP and ST degradation can influence the performance and health of dairy cows, but data that can enable the comparison of ruminal degradation within and between barley, rye, and triticale grains are scarce. Commonly used techniques to explore ruminal degradation of feed are in situ and in vitro incubations. Both techniques require ruminal-fistulated animals, but alternative methods are being demanded by the community, in order to reduce the number of animal trials. An approach with the potential to estimate the nutritional value of various feeds is near-infrared spectroscopy (NIRS). The present thesis has two major parts. In the first part, ruminal degradation parameters and the effective degradability (ED) of DM, CP, and ST from barley, rye, and triticale grains are investigated using standardised in situ and in vitro incubation techniques. A total of 20 genotypes per grain species were used. In the second part, NIRS calibrations were developed with the aim of estimating the CP and ST concentrations of cereal grains and their incubation residues. Subsequently, data from in situ experiments were used to establish the calibrations for estimating the ruminal in situ degradation of cereal grains from their spectral data. In situ degradation studies have been conducted by ruminal incubation, utilising three lactating cows. Ruminal degradation parameters and ED (ruminal passage rate = 8%//h) were calculated. For in vitro incubations, the samples were incubated in a rumen fluid-buffer mixture (‘Hohenheim Gas Test’). The gas production was recorded for estimating gas production kinetics. In vitro gas production—in combination with crude nutrient concentrations—was used to estimate the metabolisable energy concentration (ME) and digestibility of organic matter (dOM). The degradation rates differed between and within the grain species for DM, CP, and ST. The variation within grain species was not reflected in the ED of CP and ST, due to the relatively fast and almost complete degradation of the grains. The ED of CP was 77% (69–80%) for barley, 85% (83–86%) for rye, and 82% (79–84%) for triticale. The corresponding ED of ST was 86% (82–88%), 95% (92–96%), and 94% (90–95%). Accordingly, the estimated ME (barley: 13.5 MJ/kg DM, rye: 13.9 MJ/kg DM, triticale: 13.5 MJ/ kg DM) showed only relatively minor variation within one grain species. The dOM was overall at a high level (barley: 91.3%, rye: 95.3%, triticale: 95.8%). The relatively small variation within one grain species could not be explained by the chemical and physical characteristics of the samples. Hence, it was concluded that it is feasible to use mean values for every species in feed formulation and ration planning. In the second part of this thesis, it was shown that it is possible to replace chemical CP and ST analyses of samples from in situ studies by NIRS without affecting the calculated ruminal degradation characteristics. NIRS could be used to estimate the ED of CP and ST from cereal grains. The sample set to establish the calibrations included barley, durum, maize, rye, triticale, and wheat grains. Calibrations for the CP and ST concentration were extended to pea samples. The calibrations with the best validation performance for CP and ST concentration were obtained by using the wavelength segment of 1250 to 2450 nm and the first derivative of the spectra (CP: R2 = 0.99; SEP = 0.46% DM. ST: R2 = 0.99; SEP = 2.10% DM). The results of in situ studies did not differ, irrespective of whether chemical or NIRS analysis was used. Like the CP and ST concentration, the ED was estimated with a high accuracy (ED8 CP: R2 = 0.95; SEP = 2.43%. ED8 ST: R2 = 0.97; SEP = 2.45%). However, calibrations need to be extended before they can be recommended for routine use. The present thesis demonstrates that the ED of CP and ST of barley, rye, and triticale grains differ between the species, but variation within one grain species is relatively small and not related to the chemical and physical characteristics of the grain. Hence, under the prevailing cultivation conditions, the mean values for each grain species in feed evaluation are deemed adequate. It was demonstrated that NIRS has the potential to facilitate the evaluation of the nutritive value of cereal grains for ruminants.
Rye (Secale cereale L.) : agronomic performance under drought and methods of crop physiology to determine the drought tolerance of winter rye
(2015) Kottmann, Lorenz; Fangmeier, Andreas
Winter rye (Secale cereale L.) is predominantly cultivated on light and sandy soils with a low water holding capacity and will therefore be especially affected by drought induced yield losses in Central and Eastern Europe in the future. Drought adaption through breeding is therefore an important task in order to adapt this crop to future climate conditions. In this context, the crop physiology methods canopy temperature depression (CTD = Tair - Tcanopy) and carbon isotope discrimination (delta) were examined for their suitability as selection criterion under drought on a small number of genotypes. Two sets of each 16 genotypes were therefore grown under different drought conditions in rain-out shelters and under well-watered conditions in the years 2011, 2012, and 2013. The CTD was determined several times during the growth period using two infrared (IR) thermometers and an IR camera. delta-analyses were performed on mature flag leaves (delta_leaf) and grains (delta_grains). Furthermore, ash content in mature flag leaves and grains, as well as mineral concentrations in mature flag leaves (Ca, K, Mg, and Si) were examined for their use as surrogates for the expensive and time-consuming delta-analyses. In addition to the evaluation of possible selection criterions, the agronomic performance of rye in the different drought regimes was assessed: Grain-, straw-, and total aboveground biomass yields, the grain yield components spikes m-2, kernels spike-1, and thousand kernel weight (TKW), leaf area index (LAI), and phenological characteristics were examined. Drought induced grain yield reductions ranged from 14 to 57%, whereas straw yield was generally lesser affected. The growth period was shortened by up to 12 days under drought conditions compared to optimal water supply. Grain yield was positively associated to straw yield, LAI, spikes m-2, and kernels spike-1 under water deficit. High number of grains per area land seemed to be especially important for high grain yields under drought. Furthermore, the results suggest a strong importance of pre-anthesis reserves for the reallocation of assimilates for grain filling under drought in rye. Regarding the suitability of possible selection criterions, CTD was significantly positively related to grain yield under drought. Significant correlations between CTD and grain yield were, however, only observed when the measurements were carried out on days with optimal weather conditions. Optimal conditions turned out to be days with a clear sky, a solar irradiation >700 W m-2, an air temperature of at least 20°C, as well as wind speeds <3 m s-1. Furthermore, the results showed that also rather inexpensive IR instruments are suitable to assess the CTD. Regarding the carbon isotope discrimination, delta_leaf was significantly positively related to grain yield under water deficit, but the correlation was weaker than between CTD and grain yield. Delta_grains was not related to grain yield at all. Ash content and mineral concentrations were significantly related to grain yield under drought, but the correlations were quite inconsistent between the two experimental years. Because of the weak or missing relationship with grain yield, carbon isotope discrimination and its potential surrogates ash content and mineral concentration cannot be recommended for their use as selection criterions under German climate conditions at present. A general limitation of the preset work was, however, the low genetic variability of the genotypes, which may have reduced the significance of the results. The results should therefore be validated with a more diverse set of genotypes. However, especially the CTD seemed to be a promising selection criterion which may help to develop drought tolerant rye genotypes, if this method can be successfully integrated into the breeding process.
Theoretical and experimental investigations on the exploitation of heterosis in hybrid breeding
(2009) Fischer, Sandra; Melchinger, Albrecht E.
Hybrid breeding has played a key role in the improvement of the productivity of many crops. Genetic variability, an essential prerequisite in plant breeding, is expected to decrease in heterotic groups as a result of continuous breeding efforts. The consequences of the narrowing of genetic variability are a decrease in selection gain and an increase in the susceptibility of cultivars. Thus, establishment of heterotic groups and broadening the genetic base of established heterotic groups are very important research topics in hybrid breeding. Our objectives were to (1) evaluate heterosis in winter triticale and identify heterotic groups based on field and SSR marker data, (2) investigate by field evaluations and SSR markers the heterotic relationships between the Central European heterotic groups in maize and rye and exotic germplasm from the US and Eastern Europe, respectively, and (3) monitor temporal changes over 30 years in the magnitude of variances due to general combining ability (GCA) and specific combining ability (SCA) in an applied hybrid maize breeding program. Triticale has low heterosis and, therefore, no hybrid cultivars have been developed, although an effective CMS system is available. Twenty-one lines and their 210 diallel crosses were field-evaluated for grain yield at five locations in Germany. 95 SSR markers were used to analyze the parents for identifying two diverse subgroups. Hybrid performance, midparent heterosis, and estimates of variance due to GCA and SCA were determined in a diallel, a 10 × 11 factorial, and the remaining two sub-diallels with 10 and 11 parents. In addition, we applied an enumeration algorithm, which explored the entire sample space to identify diverse heterotic groups and optimize different criteria in this context. The ratio of variance due to GCA to variance due to SCA was higher for factorials between groups of parents than in diallels and subdiallels within groups. The analyses indicated a more favorable ratio in situations with genetically distinct populations compared to situations with genetically less distinct populations. Application of the enumeration algorithm improved all criteria. F1 performance followed by heterosis were the most important criteria for development and enrichment of heterotic groups. Introgression of new germplasm to broaden the genetic base of heterotic groups is required to ensure continued genetic gains in hybrid breeding. In maize, we evaluated 19 inbreds belonging to two Central European heterotic groups and US heterotic groups and their factorial crosses in F1 and F2 generations for grain yield and dry matter concentration. The parental inbreds were additionally fingerprinted with 266 SSR markers. Multi-environment evaluation was performed in three mega-environments: Central Europe, US Cornbelt, and Southeast Europe. We found higher genetic diversity in the exotic germplasm than in the Central European heterotic groups. Based on F1 performance and heterosis, we conclude that non-Stiff Stalk germplasm should be introgressed into the Flint group and the Stiff Stalk germplasm into the Dent group. In rye, we evaluated testcrosses of 610 S0 clones belonging to the two Central European heterotic groups and five East European open-pollinated varieties (OPVs). S0 clones were fingerprinted with 30 SSR markers. We found higher genetic diversity in the OPVs compared to the Central European heterotic groups. The Carsten group had a narrow genetic base and should, therefore, be the primary target for genetic broadening. Nevertheless, all five OPVs were genetically closer to Petkus than Carsten. Two OPVs were identified as good candidates for introgression into Petkus and one into Carsten. We suggest to use selected clones of these populations for introgression. Continuous selection is expected to narrow the genetic base of heterotic groups over time. We studied the nature and magnitude of genetic variability in the breeding materials of the maize program of the University of Hohenheim, which is based on two heterotic groups with continuous enrichment by other germplasm. The data generated in multilocation field trials based on inter-group factorial designs conducted from 1975 to 2004 for grain yield and dry matter concentration were analyzed. There was neither a decrease in the magnitude of genetic variance nor a change in the predominance of variance due to GCA over variance due to SCA. Consequently, for avoiding the adverse effects of selection on genetic variation and for ensuring medium and long-term selection gains, heterotic groups should not be treated as closed populations, but should be continuously enriched by introgression of new germplasm.
Wirkung rassenspezifischer Braunrostresistenzen in genetisch diversifizierten Roggenpopulationen
(2004) Wilde, Katinka; Miedaner, Thomas
Leaf rust (Puccinia recondita f.sp. secalis) is the most frequently occuring leaf disease in German winter rye (Secale cereale L.). To test the usefulness and potentially prolong the durability of race-specific resistance genes, we increased host complexity and diversity by producing synthetic (Syn) populations segregating for one to four resistance sources as a model system for hybrid varieties. Thirty synthetics were grown together with three highly susceptible synthetics as checks, two Russian full-sib families (FSF), a leaf-rust-resistant-hybrid variety, a set of 17 differential genotypes and ten parental lines at six locations in three years (17 environments) in Germany under natural infection. The parental lines were only sown in 11 environments. Disease severity of about 120 plants for each synthetic, FSF, hybrid and about 25 plants for each differential genotype and parental line was estimated as percentage of infected leaf area on the leaf below the flag leaf at the mid and the end of the natural epidemic. Susceptible synthetics showed that disease severity was similarly high in all environments. Only two out of 30 synthetics and both FSF were resistant across 17 environments. Low resistance of the synthetic was caused by the low resistance of the parental lines. Nonetheless, some of the synthetics were more resistant than the tested commercial hybrid variety. Even though the resistance was not used in practical breeding programs to date we detected virulence for each resistance gene tested. In conclusion, the German leaf rust population seems to be highly diverse and none of the self-fertile resistance sources used provided full protection. New race-specific resistances or highly effective quantitative resistances are therefore needed and should be combined.