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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.

Background: Whole plant senescence represents the final stage in the life cycle of annual plants, characterized by the decomposition of aging organs and transfer of nutrients to seeds, thereby ensuring the survival of next generation. However, the transcriptomic profile of vegetative organs during this death process remains to be fully elucidated, especially regarding the distinctions between natural programmed death and artificial sudden death induced by herbicide. Results: Differential genes expression analysis using RNA-seq in leaves and roots of Arabidopsis thaliana revealed that natural senescence commenced in leaves at 45–52 days after planting, followed by roots initiated at 52–60 days. Additionally, both organs exhibited similarities with artificially induced senescence by glyphosate. Transcription factors Rap2.6L and WKRY75 appeared to serve as central mediators of regulatory changes during natural senescence, as indicated by co-expression networks. Furthermore, the upregulation of RRTF1, exclusively observed during natural death, suggested its role as a regulator of jasmonic acid and reactive oxygen species (ROS) responses, potentially triggering nitrogen recycling in leaves, such as the glutamate dehydrogenase (GDH) shunt. Root senescence was characterized by the activation of AMT2;1 and GLN1;3, facilitating ammonium availability for root-to-shoot translocation, likely under the regulation of PDF2.1. Conclusions: Our study offers valuable insights into the transcriptomic interplay between phytohormones and ROS during whole plant senescence. We observed distinct regulatory networks governing nitrogen utilization in leaf and root senescence processes. Furthermore, the efficient allocation of energy from vegetative organs to seeds emerges as a critical determinant of population sustainability of annual Arabidopsis. [ABSTRACT FROM AUTHOR]

Angelica hirsutiflora Liu et al.1961, is a perennial herb in the Apiaceae family that is endemic to Taiwan. In this study, the complete circular chloroplast genome of A. hirsutiflora was reconstructed and annotated using Illumina sequencing. The size of the chloroplast genome is 154,266 bp, consisting of two inverted repeats (IRs, 25,075 bp) separated by a large single-copy region (LSC, 86,569 bp) and a small single-copy region (SSC, 17,547 bp). The GC content of the chloroplast genome is 37.6%. There are 114 different genes in the chloroplast genome of A. hirsutiflora, including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that A. hirsutiflora forms a distinct clade, and separated from other species within the genus Angelica. This study provided insights into the evolutionary relationships among different species of Angelica. [ABSTRACT FROM AUTHOR]

Flowering phenology of alpine plant communities and seasonal dynamics of flower visitors have been scarcely studied in the tropical/subtropical alpine regions. We report flowering phenology, flower production, and flower‐visiting insects in an alpine site of central Taiwan. Throughout the research period (2017–2018), we recorded flowering phenology of 130 plant species, flower production of 81 species, and 15,127 insects visiting alpine flowers. Most of the alpine plants were visited by dipteran insects and/or hymenopteran insects. The seasonal patterns of flowering were more apparent in bee‐visited plants compared to fly‐visited plants in which the flowering of bee‐visited plants clearly increased as the season progressed. About 63% of flower visitors were dipteran insects (syrphid and non‐syrphid flies), and 30% were hymenopteran insects (mostly bumble‐bee workers). Although the seasonal trend in fly abundance was less clear between years, bumble‐bee abundance consistently increased in the middle to late seasons, reflecting colony development. There was a positive correlation between bee abundance and the number of flowering species of bee‐visited plants, but there was no correlation between fly abundance and the number of flowering species of fly‐visited plants throughout the season. These results suggest that the flowering phenology of subtropical alpine communities is influenced by the seasonal availability of pollinators. Bumble bees, syrphid flies, and non‐syrphid flies had wide ranges of foraging flowers, but their niche overlap was relatively small. Because cold‐adapted bumble bees are threatened by climate change in Taiwan, plant–pollinator interactions may be disturbed by global warming. [ABSTRACT FROM AUTHOR]

Background: While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. Results: Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. Conclusions: The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution. [ABSTRACT FROM AUTHOR]

Background and Aims Germplasm with diverse, agronomically relevant traits forms the foundation of a successful plant breeding programme. Since 1993, the United Nations has been advocating the implementation of the Convention on Biological Diversity (CBD) and the subsequent 2002 Bonn Guidelines as international best practice on germplasm collection and use. In 2006, a European team made an expedition to Asia to collect wild germplasm of Miscanthus , a C4 perennial rhizomatous grass, for breeding an environmentally adaptable, resilient and high-yielding bioenergy crop. We outline general aspects of germplasm collection, conservation, breeding and biomass production evaluation while following the CBD's guidelines, respecting biodiversity and conservation needs, and the ethical use of genetic resources. Methods Effective protocols, quarantine, methods for collecting seed and rhizomes, and a genebank for conservation were established. Versatile informatics and database architecture were used to assist in selection, flowering synchronization, crossing, evaluation, phenotyping and data integration. Approaches were formulated to comply with the CBD guidelines. Key Results A total of 303 accessions of M. sinensis , M. sacchariflorus and M. floridulus were collected from 158 geographically and environmentally diverse locations. These species were shown to accumulate different amounts of aerial biomass due to combinations of stem count, height and thickness. Progeny from one interspecies cross accumulated more biomass in early trials and has shown double the yield performance in years 3–4 compared with the existing commercial cultivar M. × giganteus. An example of an F1 hybrid has already demonstrated the long-term potential of exploiting this collection for a breeding programme. Conclusions By conforming to the CBD principles, the authors' international collaboration provides a practical example of implementing the CBD. The collection widened the genetic diversity of Miscanthus available to allow for breeding of novel hybrids that exhibit more diverse traits to increase yield and resilience for growth on marginal land and in climate-challenged environments. [ABSTRACT FROM AUTHOR]

Field trials in Europe with Miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M. × giganteus ( M × g) combine both high yield potentials and low inputs in a wide range of soils and climates. Miscanthus hybrids are expected to play a major role in the provision of perennial lignocellulosic biomass across much of Europe as part of a lower carbon economy. However, even with favourable policies in some European countries, uptake has been slow. M × g, as a sterile clone, can only be propagated vegetatively, which leads to high establishment costs and low multiplication rates. Consequently, a decade ago, a strategic decision to develop rapidly multiplied seeded hybrids was taken. To make progress on this goal, we have (1) harnessed the genetic diversity in Miscanthus by crossing and progeny testing thousands of parental combinations to select several candidate seed-based hybrids adapted to European environments, (2) established field scale seed production methods with annual multiplication factors >1500×, (3) developed the agronomy for establishing large stands from seed sown plug plants to reduce establishment times by a year compared to M × g, (4) trialled a range of harvest techniques to improve compositional quality and logistics on a large scale, (5) performed spatial analyses of yield potential and land availability to identify regional opportunities across Europe and doubled the area within the bio-climatic envelope, (6) considered on-farm economic, practical and environmental benefits that can be attractive to growers. The technical barriers to adoption have now been overcome sufficiently such that Miscanthus is ready to use as a low-carbon feedstock in the European bio-economy. [ABSTRACT FROM AUTHOR]

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/ sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10−9 to 1.20 × 10−6, resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow. [ABSTRACT FROM AUTHOR]

Angelica hirsutiflora Liu et al.1961, is a perennial herb in the Apiaceae family that is endemic to Taiwan. In this study, the complete circular chloroplast genome of A. hirsutiflora was reconstructed and annotated using Illumina sequencing. The size of the chloroplast genome is 154,266 bp, consisting of two inverted repeats (IRs, 25,075 bp) separated by a large single-copy region (LSC, 86,569 bp) and a small single-copy region (SSC, 17,547 bp). The GC content of the chloroplast genome is 37.6%. There are 114 different genes in the chloroplast genome of A. hirsutiflora , including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that A. hirsutiflora forms a distinct clade, and separated from other species within the genus Angelica . This study provided insights into the evolutionary relationships among different species of Angelica ., Competing Interests: The authors report no potential conflicts of interest. This is to acknowledge any financial interest or benefit that has arisen from the direct applications of your research., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Fermented soy sauce consists of microorganisms that exert beneficial effects. However, the microbial community dynamics during the fermentation course is poorly characterized. Soy sauce production is classified into the stages of mash fermentation with koji (S0), brine addition (S1), microbial transformation (S2), flavor creation (S3), and fermentation completion (S4). In this study, microbial succession was investigated across stages at different temperatures using metagenomics analyses. During mash fermentation, Aspergillus dominated the fungal microbiota in all stages, while the bacterial composition was dominated by Bacillus at room temperature and by a diverse composition of enriched lactic acid bacteria (LAB) at a controlled temperature. Compared with a stable fungal composition, bacterial dynamics were mostly attributable to fluctuations of LAB, which break down carbohydrates into lactic acid. After adding brine, increased levels of Enterococcus and decreased levels of Lactococcus from S1 to S4 may reflect differences in salinity tolerance. Staphylococcus , as a fermentation starter at S0, stayed predominant throughout fermentation and hydrolyzed soybean proteins. Meanwhile, Rhizopus and Penicillium may improve the flavor. The acidification of soy sauce was likely attributable to production of organic acids by Bacillus and LAB under room temperature and controlled temperature conditions, respectively. Metagenomic analysis revealed that microbial succession was associated with the fermentation efficiency and flavor enhancement. Controlled temperature nurture more LAB than uncontrolled temperatures and may ensure the production of lactic acid for the development of soy sauce flavor., Competing Interests: The authors declare no conflicts of interests., (©2023 BMFH Press.)

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)