Solving the mystery of Obake rice in Africa: population structure analyses of reveal three genetic groups and evidence of both recent and ancient introgression with .

The undomesticated rice relative is a valuable genetic resource for the improvement of the domesticated Asian rice, . To facilitate the conservation, management, and use of germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between and . Though past plant breeding efforts to introgress genes from have improved biotic stress resistance, ratooning ability, and yield in , progress has been limited by substantial breeding barriers.

Similar photosynthetic but different yield responses of C and C crops to elevated O.

The deleterious effects of ozone (O) pollution on crop physiology, yield, and productivity are widely acknowledged. It has also been assumed that C crops with a carbon concentrating mechanism and greater water use efficiency are less sensitive to O pollution than C crops. This assumption has not been widely tested.

Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids.

Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity.

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome.

Background: Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes.

Results: Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities.

Genome-wide association analysis for emergence of deeply sown rice () reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field.

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.

Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits.

Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable.

Transformation and gene editing in the bioenergy grass Miscanthus.

Background: Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M.

The leaf economics spectrum of triploid and tetraploid C grass Miscanthus x giganteus.

The leaf economics spectrum (LES) describes multivariate correlations in leaf structural, physiological and chemical traits, originally based on diverse C species grown under natural ecosystems. However, the specific contribution of C species to the global LES is studied less widely. C species have a CO concentrating mechanism which drives high rates of photosynthesis and improves resource use efficiency, thus potentially pushing them towards the edge of the LES.

A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.

Background: Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.

Testing unified theories for ozone response in C species.

There is tremendous interspecific variability in O  sensitivity among C  species, but variation among C  species has been less clearly documented. It is also unclear whether stomatal conductance and leaf structure such as leaf mass per area (LMA) determine the variation in sensitivity to O across species. In this study, we investigated leaf morphological, chemical, and photosynthetic responses of 22 genotypes of four C bioenergy species (switchgrass, sorghum, maize, and miscanthus) to elevated O in side-by-side field experiments using free-air O concentration enrichment (FACE).

Characterization of the Flowering Time Gene in a Mini-Core Collection of .

The optimal flowering time for bioenergy crop is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in . Here, we report on the sequence characterization and gene expression of , a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height.

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.

Screening of Allelochemicals in Extracts and Assessment of Their Effects on Germination and Seedling Growth of Common Weeds.

There is increasing interest in the application of bioherbicides because they are less destructive to the global ecosystem than synthetic herbicides. Research has focused on reducing the dependence upon synthetic herbicides by substituting them with environmentally and economically sustainable bioproducts. Allelopathic phytochemicals may be an efficient method for controlling weeds, benefitting both the environment and human health.

Training Population Optimization for Genomic Selection in .

is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies × (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species (Msi) and (Msa) could theoretically be used as training sets for genomic prediction of M×g clones with optimal genomic estimated breeding values for biofuel traits.

Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar.

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 (switchgrass), species of the genera (miscanthus), (willow) and (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.

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea.

Background And Aims: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M.

Determination of hemicellulose, cellulose and lignin content using visible and near infrared spectroscopy in Miscanthus sinensis.

Lignocellulosic components including hemicellulose, cellulose and lignin are the three major components of plant cell walls, and their proportions in biomass crops, such as Miscanthus sinensis, greatly impact feed stock conversion to liquid fuels or bio-products. In this study, the feasibility of using visible and near infrared (VIS/NIR) spectroscopy to rapidly quantify hemicellulose, cellulose and lignin in M. sinensis was investigated.

Determination of Leaf Water Content by Visible and Near-Infrared Spectrometry and Multivariate Calibration in .

Leaf water content is one of the most common physiological parameters limiting efficiency of photosynthesis and biomass productivity in plants including . Therefore, it is of great significance to determine or predict the water content quickly and non-destructively. In this study, we explored the relationship between leaf water content and diffuse reflectance spectra in .

Application of visible and near-infrared spectroscopy to classification of Miscanthus species.

The feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M.

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M.

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.

Background: In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine.

Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago.

The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1.