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The dataset contains the sequencing output (DNA variants) of targeted sequencing with Single Primer Enrichment Technology (SPET) performed on 252 samples belonging to Vicia faba L., in VCF format. The accessions were collected from the Centre for Genetic Resources located in Wageningen, Netherlands. Please note that in this variant calling file each genotyped sample represents a pool of 10 plants.

Miscanthus, a C4 perennial rhizomatous grass, is a low-input energy crop suitable for marginal land, which cultivation can improve soil quality and promote soil organic carbon (SOC) sequestration. In this study, four promising Miscanthus hybrids were chosen to evaluate their short-term potential, in six European marginal sites, to sequester SOC and improve physical, chemical, and biological soil quality in topsoil. Overall, no differences among Miscanthus hybrids were detected in terms of impacts on soil quality and SOC sequestration. SOC sequestration rate after 4 years was of +0.4 Mg C ha−1 year−1, but land-use transition from former cropland or grassland showed contrasting SOC sequestration trajectories. In unfertilized marginal lands, cultivation of high-yielding Miscanthus genotypes caused a depletion of K (−216 kg ha−1 year−1), followed by Ca (−56 kg ha−1 year−1), Mg (−102 kg ha−1 year−1) and to a lesser extent of N. On the contrary, the biological turnover of organic matter increased the available P content (+164 kg P2O5 ha−1 year−1). SOC content was identified as the main driver of changes in biological soil quality. High input of labile plant C stimulated an increment of microbial biomass and enzymatic activity. Here, a novel approach was applied to estimate C input to soil from different Miscanthus organs. Despite the high estimated plant C input to soil (0.98 Mg C ha−1 year−1), with significant differences among sites and Miscanthus hybrids, it was not identified as a driver of SOC sequestration. On the contrary, initial SOC and nutrients (N, P) content, as well as their elemental stoichiometric ratios with C, were the key factors controlling SOC dynamics. Introducing Miscanthus on marginal lands impacts positively soil biological quality over the short term, but targeted fertilization plans are needed to secure crop yield over the long term as well as the C sink capacity of this perennial cropping system.

Miscanthus is a perennial grass suitable for the production of lignocellulosic biomass on marginal lands. The effects of salt stress on Miscanthus cell wall composition and its consequences on biomass quality have nonetheless received relatively little attention. In this study, we investigated how exposure to moderate (100 mM NaCl) or severe (200 mM NaCl) saline growing conditions altered the composition of both primary and secondary cell wall components in the stems of 15 Miscanthus sinensis genotypes. The exposure to stress drastically impacted biomass yield and cell wall composition in terms of content and structural features. In general, the observed compositional changes were more pronounced under severe stress conditions and were more apparent in genotypes with a higher sensitivity towards stress. Besides a severely reduced cellulose content, salt stress led to increased pectin content, presumably in the form of highly branched rhamnogalacturonan type I. Although salt stress had a limited effect on the total lignin content, the acid-soluble lignin content was strongly increased in the most sensitive genotypes. This effect was also reflected in substantially altered lignin structures and led to a markedly reduced incorporation of syringyl subunits and p-coumaric acid moieties. Interestingly, plants that were allowed a recovery period after stress ultimately had a reduced lignin content compared to those continuously grown under control conditions. In addition, the salt stress-induced cell wall alterations contributed to an improved enzymatic saccharification efficiency.

Plant cell walls of Poaceae and eudicots differ substantially, both in the content and composition of their components. However, the genomic and genetic basis underlying these differences is not fully resolved. In this research, we analyzed multiple genomic properties of 150 cell wall gene families across 169 angiosperm genomes. The properties analyzed include gene presence/absence, copy number, synteny, occurrence of tandem gene clusters, and phylogenetic gene diversity. Results revealed a profound genomic differentiation of cell wall genes between Poaceae and eudicots, often associated with the cell wall diversity between these plant groups. For example, overall patterns of gene copy number variation and synteny were clearly divergent between Poaceae and eudicot species. Moreover, differential Poaceae–eudicot copy number and genomic contexts were observed for all the genes within the BEL1-like HOMEODOMAIN 6 regulatory pathway, which respectively induces and represses secondary cell wall synthesis in Poaceae and eudicots. Similarly, divergent synteny, copy number, and phylogenetic gene diversification were observed for the major biosynthetic genes of xyloglucans, mannans, and xylans, potentially contributing to the differences in content and types of hemicellulosic polysaccharides differences in Poaceae and eudicot cell walls. Additionally, the Poaceae-specific tandem clusters and/or higher copy number of PHENYLALANINE AMMONIA-LYASE, CAFFEIC ACID O-METHYLTRANSFERASE, or PEROXIDASE genes may underly the higher content and larger variety of phenylpropanoid compounds observed in Poaceae cell walls. All these patterns are discussed in detail in this study, along with their evolutionary and biological relevance for cell wall (genomic) diversification between Poaceae and eudicots.

Perennial biomass crops (PBCs) can potentially contribute to all ten Common Agricultural Policy (2023-27) objectives and up to eleven of the seventeen UN Sustainable Development Goals. This paper discusses interlinked issues that must be considered in the expansion of PBC production: i) available land; ii) yield potential; iii) integration into farming systems; iv) research and development requirements; v) utilisation options; and vi) market systems and the socio-economic environment. The challenge to create development pathways that are acceptable for all actors, relies on measurement, reporting and verification of greenhouse gas emissions reduction in combination with other environmental, economic and social aspects. This paper makes the following policy recommendations to enable greater PBC deployment: 1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; 2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low carbon bioenergy and bio-products; 3) support innovation in biomass utilisation value chains; and 4) continue long-term, strategic research and development and education for positive environmental, economic and social sustainability impacts.

Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023–27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&D and education for positive environmental, economic and social

New biomass crop hybrids for bioeconomic expansion require yield projections to determine their potential for strategic land use planning in the face of global challenges. Our biomass growth simulation incorporates radiation interception and conversion efficiency. Models often use leaf area to predict interception which is demanding to determine accurately, so instead we use low-cost rapid light interception measurements using a simple laboratory-made line ceptometer and relate the dynamics of canopy closure to thermal time, and to measurements of biomass. We apply the model to project the European biomass potentials of new market-ready hybrids for 2020–2030. Field measurements are easier to collect, the calibration is seasonally dynamic and reduces influence of weather variation between field sites. The model obtained is conservative, being calibrated by crops of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020–2030 based on 10% land use conversion of the least (productive) grassland and arable for farm diversification, which show a European potential of 80.7–89.7 Mt year−1 biomass, with potential for 1.2–1.3 EJ year−1 energy and 36.3–40.3 Mt year−1 carbon capture, with seeded Miscanthus sacchariflorus × sinensis displaying highest yield potential. Simulated biomass projections must be viewed in light of the field measurements on less productive land with high soil water deficits. We are attempting to model the results from an ambitious and novel project combining new hybrids across Europe with agronomy which has not been perfected on less productive sites. Nevertheless, at the time of energy sourcing issues, seed-propagated miscanthus hybrids for the upscaled provision of bioenergy offer an alternative source of renewable energy. If European countries provide incentives for growers to invest, seeded hybrids can improve product availability and biomass yields over

Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023–27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&D and education for positive environmental, economic and social

Fungal pretreatment of plant biomass is often assessed by using single plant genotypes and single fungal strains, but can the process be improved by harmonizing both, thus selecting specific substrate-fungus combinations? To tackle this question, we treated four Miscanthus sinensis genotypes with four Ceriporiopsis subvermispora strains and thoroughly analyzed substrates and treated residues. The M. sinensis genotypes differed in cellulose, hemicellulose, and lignin contents and lignin-wise diverged in subunit and linkage composition and the incorporation of hydroxycinnamic acids and tricin. Independently of the M. sinensis genotype used, C. subvermispora strain MES13904 outperformed the other three strains in extent and selectivity of delignification and consistently generated the highest enzymatic residual carbohydrate conversion and structural changes in the residual lignin. The “best” substrate-fungus combination gave 63% w/w delignification and a total enzymatic glucose yield of 66% w/w, while the “worst” combination led to 3% w/w lignin removal only and negligible glucose yield improvement. Our study highlights that white-rot fungal treatment of plant biomass is driven by both compositional and structural features of the substrate as well as the genetic makeup of the fungal strain used. These insights contribute to expediting the biological valorization of lignocellulose and ultimately to enabling more controlled fungal pretreatments.