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Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Wheat landraces are locally adapted populations that are suitable for low-input agronomic management and constraining pedo-climatic conditions. The productivity of landraces under high-input and optimal conditions is usually lower than modern wheat varieties. The present study compared the response of Sicilian wheat landraces and modern varieties to organic management, including organic fertilization, and conventional management, including mineral fertilization and chemical weed control, under rainfed condition and supplementary irrigation in a field trial conducted on a xerofluvent soil in a semiarid Mediterranean climate. Modern varieties were on average more productive than landraces, although certain landraces achieved comparable yields, in particular under organic management. The increase in grain yield under conventional management in comparison with the organic management was higher for modern varieties than landraces. The loss of productivity in rainfed conditions was lower for landraces compared to modern varieties. The grain quality traits were similar between landraces and modern varieties and in both cases the conventional management led to an improvement of the traits. These findings highlight the resilience and adaptability of traditional wheat landraces to low-input agricultural systems and offer valuable insights into improving the sustainability and productivity of wheat production in Mediterranean environments. [ABSTRACT FROM AUTHOR]

The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g. by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialized methods for the identification of orthologs to short proteins and noncoding RNAs and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the findable, accessible, interoperable, and reusable (FAIR) principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution. [ABSTRACT FROM AUTHOR]

The dwindling availability of agricultural land, caused by factors such as rapid population growth, urban expansion, and soil contamination, has significantly increased the pressure on food production. To address this challenge, cultivating non-food crops on contaminated land has emerged as a promising solution. This approach not only frees up fertile soil for food production but also mitigates human exposure to contaminants. This work aimed to examine the impact of soil contamination with Cd, Pb, Ni, and Zn on the growth, productivity, metal accumulation, and the tolerance of five lignocellulosic non-food crops: switchgrass (Panicum virgatum L.), biomass sorghum (Sorghum bicolor L. Moench), giant reed (Arundo donax L.), African fodder cane (Saccharum spontaneum L. spp. aegyptiacum Willd. Hackel), and miscanthus (Miscanthus × giganteus Greef et Deu.). A two-year pot experiment was conducted in Greece, Italy, and Portugal, following the same protocols and applying various levels of metals: Cd (0, 4, 8 mg kg−1), Pb and Zn (0, 450, 900 mg kg−1), and Ni (0, 110, 220 mg kg−1). The experimental design was completely randomized, with three replicates for each treatment. The results showed that switchgrass and sorghum generally maintained their height and productivity under Cd and Pb stress but were adversely affected by high Zn and Ni concentrations. Giant reed and African fodder cane showed reduced height and productivity at higher Ni and Zn levels. Miscanthus exhibited resilience in height but experienced productivity reductions only at the highest Zn concentration. Heavy metal uptake varied among crops, with switchgrass and sorghum showing high Cd and Pb uptake, while giant reed accumulated the most Cd and Zn. Miscanthus had the highest Ni accumulation. The tolerance indices indicated that switchgrass and sorghum were more tolerant to Cd and Zn at lower concentrations, whereas miscanthus had lower tolerance to Cd but a higher tolerance to Zn at higher concentrations. Giant reed and African fodder cane demonstrated stable tolerance across most heavy metals. Accumulation indices highlighted the effectiveness of switchgrass and sorghum in Cd and Pb uptake, while miscanthus excelled in Ni and Zn accumulation. The cluster analysis revealed similar responses to heavy metal stress between African fodder cane and giant reed, as well as between sorghum and miscanthus, with switchgrass displaying distinct behavior. Overall, the study highlights the differential tolerance and accumulation capacities of these crops, indicating the potential for phytoremediation applications and biomass production in heavy metal-contaminated soils. [ABSTRACT FROM AUTHOR]

In this study, the effects of repeated cycles of drying and rehydration on some physiological traits were assessed in long shelf-life tomatoes cultivated in a typical semi-arid area of Southern Italy. Three Sicilian landraces ('Custonaci', 'Salina', and 'Vulcano') from the germplasm collection at CNR-IBE (Catania, Italy) and a commercial tomato mini-plum ('Faino Hy., control) were investigated under three water regimes: DRY (no irrigation), IRR (long-season full irrigation) and REW (post-drought rewaterings). Net photosynthetic assimilation rate (Pn), leaf transpiration (E), stomatal conductance (gs), instantaneous water use efficiency (WUEi), leaf intercellular CO2 (Ci, ppm), and leaf temperature (°C), were measured during the growing season. At harvest (late July), fruit production per plant was measured and ripened fruits were analysed for total solids (TS), soluble solids (SS), reducing sugars (RS), vitamin C (AscA), and total phenols (TP). Pn promptly responded to rewatering (REW), quickly increasing immediately after irrigation, and declined with soil drying up. All genotypes had similar physiological pathways in DRY, but in IRR, 'Faino' had higher Pn (up to 31 μmol CO2 m−2s−1) and E (up to 18 mmol H2O m−2s−1). Stomatal conductance (gs) after rewatering steeply increased and quickly declined after that. All local landraces had the same gs in IRR and REW. Variations in RWC were less pronounced than those in other physiological parameters. WUEi in REW and DRY proceeded similarly (up to 3 μmol CO2 mmol H2O). Irrigation in REW significantly promoted plant productivity over the DRY control (up to +150% in 'Vulcano'). TS and SS in REW were lower than those in DRY, but higher (+19 and +7%, respectively) than in IRR. Vitamin C was greater in DRY and REW (26 and 18% higher than in IRR, respectively). TP in all local tomatoes were significantly higher (up to +29% in 'Vulcano') than those in the commercial control. Water regime had a minor effect on TP in 'Custonaci' and 'Salina'. Principal Component Analysis (PCA) provided information on the changes in physiological and fruit quality traits in tomatoes in relation to cultivars and water regimes. The results of this study also revealed that a water-saving irrigation strategy where few irrigations are applied after prolonged periods of drought might be profitable in terms of fruit production enhancement in long shelf-life tomatoes and that limited rewaterings in most cases, help retaining high levels of fruit quality traits. [ABSTRACT FROM AUTHOR]