Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Establishment, Growth, and Yield Potential of the Perennial Grass Miscanthus × Giganteus on Degraded Coal Mine Soils.

Miscanthus × giganteus is a giant C4 grass native to Asia. Unlike most C4 species, it is relatively cold tolerant due to adaptations across a wide range of altitudes. These grasses are characterized by high productivity and low input requirements, making them excellent candidates for bioenergy feedstock production. The aim of this study was to investigate the potential for growing Miscanthus on extremely marginal soils, degraded by open lignite (brown coal) mining. Field experiments were established within three blocks situated on waste heaps originating from the lignite mine. Analyses were conducted over the first 3 years following Miscanthus cultivation, focusing on the effect of organic and mineral fertilization on crop growth, development and yield in this extreme environment. The following levels of fertilization were implemented between the blocks: the control plot with no fertilization (D0), a plot with sewage sludge (D1), a plot with an identical amount of sewage sludge plus one dose of mineral fertilizer (D2) and a plot with an identical amount of sewage sludge plus a double dose of mineral fertilizer (D3). Crop development and characteristics (plant height, tillering, and biomass yield [dry matter]) were measured throughout the study period and analyzed using Analysis of Variance (ANOVA). Significant differences were apparent between plant development and 3rd year biomass production over the course of the study (0.964 kg plant-1 for DO compared to 1.503 kg plant-1 for D1). Soil analyses conducted over the course of the experiment showed that organic carbon levels within the soil increased significantly following the cultivation of Miscanthus, and overall, pH decreased. With the exception of iron, macronutrient concentrations remained stable throughout. The promising yields and positive effects of Miscanthus on the degraded soil suggests that long term plantations on land otherwise unsuitable for agriculture may prove to be of great environmental and economic significance.

Low-temperature leaf photosynthesis of a Miscanthus germplasm collection correlates positively to shoot growth rate and specific leaf area.

BACKGROUND AND AIMS: The C4 perennial grass miscanthus has been found to be less sensitive to cold than most other C4 species, but still emerges later in spring than C3 species. Genotypic differences in miscanthus were investigated to identify genotypes with a high cold tolerance at low temperatures and quick recovery upon rising temperatures to enable them to exploit the early growing season in maritime cold climates. Suitable methods for field screening of cold tolerance in miscanthus were also identified. METHODS: Fourteen genotypes of M. sacchariflorus, M. sinensis, M. tinctorius and M. × giganteus were selected and grown under warm (24 °C) and cold (14 °C) conditions in a controlled environment. Dark-adapted chlorophyll fluorescence, specific leaf area (SLA) and net photosynthetic rate at a photosynthetically active radiation (PAR) of 1000 µmol m(-2) s(-1) (A1000) were measured. Photosynthetic light and CO2 response curves were obtained from 11 of the genotypes, and shoot growth rate was measured under field conditions. KEY RESULTS: A positive linear relationship was found between SLA and light-saturated photosynthesis (Asat) across genotypes, and also between shoot growth rate under cool field conditions and A1000 at 14 °C in a climate chamber. When lowering the temperature from 24 to 14 °C, one M. sacchariflorus exhibited significantly higher Asat and maximum photosynthetic rate in the CO2 response curve (Vmax) than other genotypes at 14 °C, except M × giganteus 'Hornum'. Several genotypes returned to their pre-chilling A1000 values when the temperature was increased to 24 °C after 24 d growth at 14 °C. CONCLUSIONS: One M. sacchariflorus genotype had similar or higher photosynthetic capacity than M × giganteus, and may be used for cultivation together with M × giganteus or for breeding new interspecies hybrids with improved traits for temperate climates. Two easily measured variables, SLA and shoot growth rate, may be useful for genotype screening of productivity and cold tolerance.

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland.

MAIN CONCLUSION: Analysis of 180 accessions of Miscanthus using a DArT platform revealed high diversity. The phylogenetic analysis revealed that M. × giganteus accessions fall into two genetically distinct groups. Miscanthus is a genus of perennial rhizomatous grasses that has emerged in last 20 years as a feedstock for bioenergy and biofuel production. Currently, the most widely used accession for bioenergy purposes is Miscanthus × giganteus, a sterile triploid hybrid between Miscanthus sinensis and Miscanthus sacchariflorus. However, previous reports have shown that genetic diversity of Miscanthus × giganteus is limited. Here, we report development of Diversity Arrays Technology platform for the analysis of genetic structure of a Miscanthus collection of 180 accessions. A total of 906 markers were obtained of which around 25.5% exhibited polymorphism information content value in the range of 0.40 and 0.50 and are considered particularly informative. Newly developed marker system will serve as an additional resource to assist crop improvement, germplasm preservation and genetic studies. Three types of analysis indicated that 180 accessions from the collection were well differentiated and presented high diversity. Interestingly, the analysis revealed that there are two separate groups of plants, significantly differing in genetic diversity, that are commercially available as M. × giganteus. We suggest that one of these groups is most likely mutants or somaclonal variants of original M. × giganteus. The other group is recent hybrids of Miscanthus of higher genetic diversity. This study indicates that the diversity of commercially available M. × giganteus is higher than commonly assumed. Development of the new marker system can significantly assist breeding of new commercial cultivars of Miscanthus for bioenergy use.

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy.

BACKGROUND: Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed. RESULTS: We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum. CONCLUSIONS: The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion.

Interaction of gene effects with environments for malting quality of barley doubled haploids.

Barley doubled haploids covering a wide range of malting quality, along with their parental cultivars and F2, F3 hybrids, were investigated in six environments (three locations, two years) to study the genotype-environment (G x E) interaction structure and the influence of environments on additive, dominance and epistatic gene effects. Grain and malt characters, such as 1000-grain weight, percentage of plump kernels, malt extract yield, protein content, Kolbach index and malt fine-coarse difference (FCD), were measured. Main effects for genetic parameters were estimated and regression analysis was used to explain the interaction of gene effects with environments. The results show that additive effects had the greatest interaction with environments for all the analysed traits, but only for malt characters this interaction was linear. Interaction of dominance effects was much lower and only in the case of 1000-grain weight, protein content and Kolbach index it proved to be significant. The results suggest that effects of heterozygous loci are more stable in contrasting environments than effects of homozygous loci.