Cell wall composition and biomass saccharification potential of Sida hermaphrodita differ between genetically distant accessions.

Due to its ample production of lignocellulosic biomass, Sida hermaphrodita (Sida), a perennial forb, is considered a valuable raw material for biorefinery processes. The recalcitrant nature of Sida lignocellulosic biomass towards pretreatment and fractionation processes has previously been studied. However, Sida is a non-domesticated species and here we aimed at expanding the potential of such plants in terms of their processability for downstream processes by making use of the natural variety of Sida. To achieve this goal, we established a collection comprising 16 different Sida accessions obtained from North America and Europe. First, we asked whether their cell wall characteristics are reflected in genetic distance or geographical distribution, respectively. A genotyping-by-sequencing (GBS) analysis resulting in a phylogenic tree based on 751 Single Nucleotide Polymorphisms (SNPs), revealed a high genetic diversity and a clear separation between accessions collected in North America and Europe. Further, all three North American accessions were separated from each other. Of the eleven European accessions, five form individual groups and six others belong to a single group. Clonal plants of seven selected accessions of American and European origin were produced and cultivated under greenhouse conditions and the resulting plant material was used for in-depth wet-chemical and spectroscopic cell wall characterization. Two accessions with contrasting cell wall characteristics were then selected and processed using the OrganoCat technology. Results of the different product yields and chemical compositions are reported. Overall, cell wall analyses revealed contrasting clusters regarding these main components between the accessions that can be related to genetic and, partly, geographical distance. Phenotypically, the accessions clustered into two groups that are not entirely overlapping with geographical origin. These results can be the basis for a targeted selection or cultivation of Sida accessions for biorefinery approaches.

Proteomics reveals potential biomarkers of seed vigor in sugarbeet.

To unravel biomarkers of seed vigor, an important trait conditioning crop yield, a comparative proteomic study was conducted with sugarbeet seed samples of varying vigor as generated by an invigoration treatment called hydropriming and an aging treatment called controlled deterioration. Comparative proteomics revealed proteins exhibiting contrasting behavior between seed samples. Thus, 18 proteins were up-regulated during priming and down-regulated during aging and further displayed an up-regulation upon priming of the aged seeds, meaning that down-regulation of these spot volumes during aging was reversible upon subsequent priming. Also, 11 proteins exhibited the converse behavior characterized by a decrease and an increase of the spot volumes during priming and aging of the control seeds, respectively, and a decrease in the spot volumes upon priming of the aged seeds. The results underpinned the role in seed vigor of several metabolic pathways involved in lipid and starch mobilization, protein synthesis or the methyl cycle. They also corroborate previous studies suggesting that the glyoxylate enzyme isocitrate lyase, the capacity of protein synthesis and components of abscisic acid signaling pathways are likely contributors of seed vigor.

Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds.

BACKGROUND: With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential. RESULTS: To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway. CONCLUSION: This study provides an important step toward the understanding of main events and metabolic pathways during germination in sugar beet. The reported alterations of gene expression in response to stress shed light on sugar beet stress adaptation mechanisms. Some of the identified stress-responsive genes provide a new potential source for improvement of sugar beet stress tolerance during germination and field emergence.

Development and QTL assessment of Triticum aestivum-Aegilops tauschii introgression lines.

A set of 84 bread wheat lines, each containing a single homozygous introgression of the Aegilops tauschii genome was produced in the 'Chinese Spring' background via backcrossing of the D-genome chromosome substitution lines 'Chinese Spring'/Sears's 'Synthetic 6x' with the recurrent parent and subsequent selfing. The development of the lines was accompanied by microsatellite marker assisted selection. With the exception of three telomeric regions at chromosomes 1DL, 4DL and 7DS, and a region of less than 24 cM on the chromosome arm 3DL, the genome of Ae. tauschii is fully represented in these lines. The newly developed lines were used for the discovery of morphological and agronomical quantitative trait loci (QTLs) from the wild species. Fifty-two introgression lines were grown in the field and evaluated for six traits including flowering time, plant height, ear length, spikelet number, fertility and grain weight per ear. Seventeen significant QTLs were detected, Ae. tauschii contributed favourable alleles at nine loci influencing five traits. The whole set of 84 homozygous lines provides a tool for further testing the effects and stability of the detected QTLs and for the evaluation of new traits.

Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags.

The genetic map of rye contains predominantly restriction fragment length polymorphism (RFLP) markers but also a limited number of microsatellite markers, which are known to be more reliable and easier to apply. We report here the saturation of the genomic map of rye with additional microsatellite-derived markers that we obtained from the rye expressed sequence tag (EST) databases and the Gatersleben collection of wheat microsatellite markers (WMS). A total of 99 loci (39 EST and 60 WMS) were mapped into the RFLP frameworks of four rye mapping populations consisting of 139, 64, 58 and 60 RFLPs, respectively. For another ten WMS loci, which amplified PCR products not polymorphic in any of the mapping populations, chromosome and chromosome arm locations were determined using wheat-rye addition lines. Chromosomes 1R, 2R, 3R, 4R, 5R, 6R and 7R were enriched with 9, 19, 9, 13, 27, 16 and 16 microsatellite loci, respectively. The microsatellite loci mapped were evenly distributed along the chromosomes, which is important for the further application of these markers for gene mapping or diversity studies in rye. Forty-four of the WMS loci mapped in rye were found to be homologous to those mapped in bread wheat ( Triticum aestivum L.).

Genetic mapping and tagging of wheat genes using RAPD, STS and SSR markers.

We applied SSR markers for mapping genes determining red coleoptile colour in wheat (Rc1, Rc2, Rc3) using F2 populations. All three genes map at about 15 to 20 cM distally from the centromere of chromosomes 7AS, 7BS and 7DS, respectively. The locations of the glume colour (Bg, Rg1) and glume hairiness (Hg) genes relative to the SSR markers of the homoeologous chromosomes group 1 were determined using molecular analysis of near-isogenic lines (NILs). One RAPD marker for the vernalisation response gene Vrn-A1 was identified by screening 95 random primers against two pairs of NILs. New PCR (STS) markers were developed based on RFLP-markers PSR426 (5A, 5B, 5D) and PSR1201 (1A, 5A, 5B). Analysis of nulli-tetrasomic and near-isogenic lines of wheat using the STS markers developed gave an indication that these new STS markers have the same chromosomal and intrachromosomal positions as the correspondent RFLP markers. Therefore, they could be used for mapping and/or tagging the vernalisation response (Vrn-A1, Vrn-B1, Vrn-D1) and homoeologous pairing (Ph1) genes.