Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC).

Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 "core" O. rufipogon and 25 "core" O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a "pre-breeding" pool for breeders attempting to incorporate novel variation into elite breeding lines.

Gasification biochar from horticultural waste: An exemplar of the circular economy in Singapore.

Organic waste, the predominant component of global solid waste, has never been higher, resulting in increased landfilling, incineration, and open dumping that releases greenhouse gases and toxins that contribute to global warming and environmental pollution. The need to create and adopt sustainable closed-loop systems for waste reduction and valorization is critical. Using organic waste as a feedstock, gasification and pyrolysis systems can produce biooil, syngas, and thermal energy, while reducing waste mass by as much as 85-95% through conversion into biochar, a valuable byproduct with myriad uses from soil conditioning to bioremediation and carbon sequestration. Here, we present a novel case study detailing the circular economy of gasification biochar in Singapore's Gardens by the Bay. Biochar produced from horticultural waste within the Gardens was tested as a partial peat moss substitute in growing lettuce, pak choi, and pansy, and found to be a viable substitute for peat moss. At low percentages of 20-30% gasification biochar, fresh weight yields for lettuce and pak choi were comparable to or exceeded those of plants grown in pure peat moss. The biochar was also analyzed as a potential additive to concrete, with a 2% biochar mortar compound found to be of suitable strength for non-structural functions, such as sidewalks, ditches, and other civil applications. These results demonstrate the global potential of circular economies based on local biochar creation and on-site use through the valorization of horticultural waste via gasification, generating clean, renewable heat or electricity, and producing a carbon-neutral to -negative byproduct in the form of biochar. They also indicate the potential of scaled-up pyrolysis or gasification systems for a circular economy in waste management.

Biochar industry to circular economy.

Biochar, produced as a by-product of pyrolysis/gasification of waste biomass, shows great potential to reduce the environment impact, address the climate change issue, and establish a circular economy model. Despite the promising outlook, the research on the benefits of biochar remains highly debated. This has been attributed to the heterogeneity of biochar itself, with its inherent physical, chemical and biological properties highly influenced by production variables such as feedstock types and treating conditions. Hence, to enable meaningful comparison of results, establishment of an agreed international standard to govern the production of biochar for specific uses is necessary. In this study, we analyzed four key uses of biochar: 1) in agriculture and horticulture, 2) as construction material, 3) as activated carbon, and 4) in anaerobic digestion. Then the guidelines for the properties of biochar, especially for the concentrations of toxic heavy metals, for its environmental friendly application were proposed in the context of Singapore. The international status of the biochar industry code of practice, feedback from Singapore local industry and government agencies, as well as future perspectives for the biochar industry were explained.

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

BACKGROUND: Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). RESULTS: Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. CONCLUSIONS: Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

Getting to the roots of it: Genetic and hormonal control of root architecture.

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Three-dimensional root phenotyping with a novel imaging and software platform.

A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform's capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P < 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture.