Recurrent selection for increased outcrossing rates of barley from semi-arid regions of Syria and Jordan

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.Die Verbesserung des Kornertrags unter Trockenstressbedingungen, wie sie beispielsweise in den semi-ariden Gebieten der sogenannten WANA-Region (West-Asien und Nord-Afrika) auftreten, stellt seit vielen Jahren ein hartnäckiges Problem dar. Obgleich Gerste (Hordeum vulgare L.) in dieser Region weitverbreitet angebaut wird, besteht eine hohe Gefahr von Ernteausfällen. Aufgrund ihrer autogamen Blühbiologie weisen Gerstensorten eine fast vollständige Homozygotie auf. Populationsgenetische Studien zeigten, dass heterozygote Gerstengenotypen eine signifikant höhere Stresstoleranz besitzen und dementsprechend sowohl im Ertragsniveau als auch in der Ertragsstabilität überlegen sind. Die Erhöhung des Heterozygotiegrades der Gerste war daher das Hauptziel dieser Arbeit. Zu diesem Zweck wurde ein neuer Ansatz der marker-gestützten rekurrenten Selektion (RS) auf hohen Heterozygotiegrad entwickelt und auf eine weltweite, genetisch diverse Gerstenkollektion angewendet. Die Ziele dieser Arbeit waren insbesondere (1) die Überprüfung der Wirksamkeit des oben genannten Ansatzes, (2) die Bestimmung des Heterozygotiegewinns über vier RS-Zyklen sowie die Evaluierung der einzelnen Selektionszyklen in einem vergleichenden Abschlußexperiment unter gemeinsamen Umweltbedingungen, (3) die Schätzung des des Selektionsdifferentials, Selektionsgewinns sowie der realisierten Heritabilität, und (4) die Bereitstellung von Gerstenmaterial mit erhöhtem Heterozygotiegrad für Pflanzenzüchtungs-programme in der WANA-Region. Der Heterozygotiegrad wurde mittels kodominanter Mikrosatellitenmarker bestimmt. Hierbei wurden nur solche Pflanzen selektiert, die Heterozygotie an möglichst vielen Markerloci aufwiesen. Es konnte dann angenommen werden, dass diese Pflanzen aus der Kreuzung zwischen einer Mutterpflanze mit genetischer Veranlagung für Offenblütigkeit und einer Bestäuberpflanze mit erhöhter Pollenschüttung hervorgegangen war. Für die Marker-auswertung wurden zunächst jeweils sechs Pflanzen in einer Mischprobe analysiert. Proben mit hohem Polymorphiegrad wurden anschließend einzelpflanzenweise genotypisiert. Um den Arbeits- und Zeitaufwand gering zu halten, kam ab dem zweiten Selecktionszyklus eine Multiplex-Analyse zum Einsatz (zwei Kombinationen zu je drei Markern). Im Verlauf des RS-Experimentes wurde eine Ausgangspopulation aus 201 Gersten-Akzessionen zusammengestellt, die aus den Sammlungen der Genbanken am International Center for Agricultural Research in Dry Areas (ICARDA) und am Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) in Deutschland stammen. Es konnte ein schrittweiser Anstieg des Heterozygotiegrades von 0,60% in der Ausgangspopulation auf 3,24% nach vier Selektionszyklen festgestellt werden. In der Ausgangspopulation zeigten die sechsreihigen Landrassen einen höheren Heterozygotiegrad als die zweireihigen. Der Selektionsgewinn war im ersten RS-Zyklus am höchsten, was auf eine starke Abnahme der genetischen Varianz im Verlauf des Experimentes sowie eine erhebliche Dezimierung des Populationsumfanges durch viele hochgradig dormante Prüfglieder nach dem ersten RS-Zyklus zurückführbar ist. Für den Heterozygotiegrad ergaben sich in den einzelnen RS-Zyklen sehr niedrige Schätzwerte der realisierten Heritabilität. Trotzdem wurde ein insgesamt signifikanter Selektionsgewinn erzielt. Zum Vergleich der in den einzelnen RS-Zyklen selektierten Fraktionen unter gemeinsamen Umweltbedingungen wurde konserviertes Saatgut in einem abschließenden Gewächshausexperiment angebaut. Neben der Heterozygotie wurden verschiedene Entwicklungs-, Blüh- und Leistungsmerkmale (Tage bis zum Ährenschieben, Antherenextrusion, offenes Abblühen, Anzahl ährentragender Halme, Hundertkorngewicht und Kornzahl je Ähre) erhoben. Die beobachtete Heterozygotie stieg von 0,30% in der C1-Population über 0,69% in C2 und C3 auf 1,29% in C4. Die unterschiede zwischen den zyklen en ueberwiegen war statistisch signifikant. Die im Abschlussexperiment festgestellten Markergenotypen wurden auch zur Schätzung der Multilocus-Auskreuzungsraten herangezogen. Die Werte stiegen von 1,4% in C1 über 2,1% in C2 auf 2,8% in C3 und C4. Der Anstieg von C1 zu C3 und C4 war signifikant. Alle Schätzwerte sind wahrscheinlich nach unten verzerrt, da während der Blüte im Gewächshaus extrem hohe Temperaturen herrschten. Große Unterschiede existierten zwischen den Auskreuzungsraten einzelner Familien innerhalb der Populationen. Es bestanden keine signifikanten Korrelationen zwischen der Auskreuzungsrate und den Blühmerkmalen. Der beobachtete positive Selektionsgewinn bekräftigt die Effektivität des hier beschriebenen Ansatzes zur Steigerung des Heterozygotiegrades beim ?Selbstbefrucher? Gerste. Hiermit eröffnen sich gute Perspektiven zur Verbesserung der Produktivität dieser Kulturart in der stressanfälligen WANA-Region. Der praktizierte Ansatz ist grundsätzlich auch auf andere autogame oder partiell autogame Nutzpflanzenarten anwendbar

Additive Manufacturing of Ceramic Materials: a Performance Comparison of Catalysts for Monopropellant Thrusters

Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass \u3ci\u3ePanicum virgatum\u3c/i\u3e

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent approximately 50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next-generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1 395 501 single nucleotide polymorphisms (SNPs), 8173 putative copy number variants and 3336 presence/absence variants. While the majority of the SNPs (84%) detected was bi-allelic, a substantial number was tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome

README

READM

genotype_means.zip

compressed zip file containing estimated genotype means in NAP (genotype_means-NAP.csv) or SAP (genotype_means-SAP.csv

An Experimental Investigation on the Rock Mechanical Behavior of Synthetic Layered Systems and Load-Cycling of its Individual Constituents

Many authors already made an attempt to understand the effect of load-cycling on material strength and the evolution of elastic parameters. However, until now there was no study on the effect of load-cycling on the evolution of elastic parameters over the complete stress strain curve, i.e. the linear elastic regime, the fracturing regime, and the fractured regime. In addition, none of the authors focussed on the effect of load-cycling on fracture network improvement. Although previous studies already showed that elastic moduli of layered systems may be determined from properties and volume fractions of its individual constituents, there is no study done on the relation between rock mechanical properties, i.e. strains and yield or failure stresses, of (synthetic) layered systems and its constituents. Furthermore, in the literature no description is found on fracture characteristics of a (synthetic) layered system. Hence, an experimental investigation is conducted on the rock mechanical behavior of synthetic layered systems subjected to increased-loading and the effect of load-cycling on its individual constituents’ rock strength, elastic parameter evolution, and fracture network improvement. The increased-loading and load-cycling rock mechanical experiments are unconfined compression tests performed at room temperature. When comparing two of the same rock materials with a maximum deviation of 1% in porosity, load-cycling leads to failure at much lower stress levels when compared to increased-loading. Within the linear elastic regime, load-cycling returns a stabilized Young’s modulus which is always larger than its envelope value, while the Poisson’s ratio of the last load cycle coincides with its envelope value. Load-cycling generates an improved fracture network when compared to increased-loading. Characteristics of the improved fracture network are the increased fracture densities and the more uniform distribution of the fractures over the volume of the material. For vertically stacked synthetic layered systems, the elastic moduli and strains can be well-predicted by the Reuss Average which uses the average rock mechanical properties and volume fractions of the individual constituents. In contrast, for synthetic layered systems the stress level at failure point is independent of the volume fractions of its constituents and is observed to be in the vicinity of its weakest constituent. Despite this, fractures are still observed in the strongest constituents. The fracture propagation through the strongest constituent is ascribed to be due to amplified stress concentrations at the tip of the propagating fracture. However, from 2-layered systems it is observed that fracture propagation through the strongest constituent depends on the thickness of the weakest constituent. At the constituents’ boundary in synthetic layered systems, there is no offset in fracture path when going from one constituent to another nor is there a sudden change in aperture. However, there is a change in fracture inclination in a way such that the fracture inclinations of the individual constituents are respected. In addition, fractures in synthetics include cataclastics over the high porous intervals (±10-25%), while the same fracture is clean over the low porous intervals (±0,5-5%).Civil Engineering and GeosciencesGeoscience & EngineeringPetroleum Engineerin

raw_phenotype.zip

compressed zip file containing raw phenotypic data in NAP (raw_phenotype-NAP.csv) or SAP (raw_phenotype-SAP.csv

formatted_SNP.zip

compressed zip file containing genotype calls at filtered SNPs in NAP and SAP (formatted_SNP.csv), NAP only (formatted_SNP-NAP.csv) or SAP only (formatted_SNP-SAP.csv

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars, three lowland and four upland, to enable comparative analyses between switchgrass cultivars and to identify single nucleotide polymorphisms (SNPs) for use in breeding and genetic analysis. We also generated individual transcript assemblies for each of the cultivars. Transcript data indicate that subgenomes of octoploid switchgrass are not substantially different from subgenomes of tetraploids as expected for an autopolyploid origin of switchgrass octoploids. Using RNA-sequencing reads aligned to the switchgrass Release 0 AP13 reference genome, we identified 1,305,976 high-confidence SNPs. Of these SNPs, 438,464 were unique to lowland cultivars, but only 12,002 were found in all lowlands. Conversely, 723,678 SNPs were unique to upland cultivars with only 34,665 observed in all uplands. Comparison of our high-confidence transcriptome-derived SNPs with SNPs previously identified in a genotyping-by-sequencing study of an association panel revealed limited overlap between the two methods, highlighting the utility of transcriptome-based SNP discovery in augmenting genome diversity polymorphism datasets. The transcript and SNP data described here provide a useful resource for switchgrass gene annotation and marker-based analyses of the switchgrass genome

Wabasso_transcript_assemblies_all_isoforms.fasta

RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso. This file includes all transcript isoforms