Plant growth promoting activity of bacteria isolated from Asian rice (Oryza sativa L.) are plant subspecies dependent

Asian rice is one of the most important crops because it is a staple food for almost half of the world's population. Rice has two subspecies, JAPONICA and INDICA. To have production of rice keep pace with a growing world population, it is anticipated that the use of fertilizers will also need to increase, which may cause environmental damage through runoff impacts. An alternative strategy to increase crop yield is the use of plant growth promoting bacteria. Thousands of microbial species can exist in association with plant roots and shoots, and some are critical to the plant's survival. We isolated 140 bacteria from rice and investigated whether JAPONICA and INDICA rice subspecies were positively influenced by these isolates. The bacterial isolates were screened for their ability to solubilize phosphate, a known plant growth promoting characteristic, and 25 isolates were selected for further analysis. These 25 phosphate solubilizing isolates were also able to produce other potentially growth-promoting factors. Five of the most promising bacterial isolates were chosen for whole genome sequencing. Four of these bacteria, isolates related to Pseudomonas mosselii, Microvirga sp., Paenibacillus rigui and Paenibacillus graminis, improved root and shoot growth, root to shoot ratio, and increased root dry weights of JAPONICA plants but had no effect on growth and development of INDICA plants. This indicates that while bacteria have several known plant growth promoting functions, their effects on growth parameters can be plant subspecies dependent and suggest close relationships between plants and their microbial partners.

Rice, Carbon Dioxide, Climate Change, And Feeding The Future

This study investigates the relationship between rice yields, climate change, and carbon dioxide (CO2). We integrate gridded climate data in the growing seasons and Asian rice yield data reported by the Food and Agriculture Organization with free air carbon dioxide enrichment (FACE) experimental data. Using those data, we estimate prediction models of rice yields that evolve over time and decompose effects of climate, CO2, and technological progress. The results show that atmospheric CO2 has significantly increased rice yields, with the contribution accounting for 29% to 33% of the observed yield growth. The results also reveal that increases in temperature decrease rice yields in parts of Asia, implying that both CO2 mitigation and climate change are yield growth depressing factors. The finding suggests a potential need for more agricultural research and development investment to offset CO2 mitigation and climate change effects.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Rice (Oryza sativa L.) is consumed by more than half of the world’s population, but despite its global importance the mechanisms of domestication remain unclear. During domestication, wild rice (O. rufipogon Griff.) was transformed by acquiring non-seed-shattering behaviour, an important genetic change that allowed humans to increase grain yield. However, we show previously identified loci, sh4 and qSH3, are individually insufficient to explain loss of seed shattering nor increases in harvest yield in wild rice. We identify the complementary interaction of key mutations for abscission layer interruption and panicle architecture that were causal in the early domestication of Asian rice. An interruption of abscission layer formation requires both sh4 and qSH3, which presents an apparent barrier to selection of shattering loss. We identified the causal single nucleotide polymorphism at qSH3 within a seed-shattering gene OsSh1 conserved in indica and japonica subspecies, but absent in the circum-aus group of rice. We demonstrate through harvest experiments that seed-shattering alone does not significantly impact yield. Instead, we observed yield increases under a SRR3-controlled closed panicle formation, which is augmented by the integration of sh4 and qSH3 alleles causing a slight inhibition of abscission layer. Complementary manipulation of seed shattering and panicle shape result in a panicle structure that is mechanically stable. We propose a stepwise route in the earliest phase of rice domestication in which selection for visible SRR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 and leading to loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 is insufficient on its own to cause abscission layer disruption and other genes, such as qSH3 are required, making mechanisms for the initial selection of non-shattering unclear. We show that shattering loss in wild rice genetic backgrounds does not increase yields. We identify an interaction in which a second trait, closed panicle formation controlled by SPR3, both increases yield and facilitates recruitment of sh4 and qSH3 which synergistically augment yield, leading to a stepwise route for rice domestication.

How gathering wild rice under human-mediated drought stress could have inadvertently paved the way to Asian rice incipient domestication and cultivation

In eastern China, on the southern end of the Yangtze Valley, early Holocene hunter-gatherers were foraging various plants, including wild rice – Oryza rufipogon Griff. – an aquatic and perennial plant which is the wild progenitor of domesticated rice. According to optimal foraging theory, these foragers should have tried to enhance the efficiency of harvesting wild rice seeds by draining water around the plants before seeds ripened and shattered. This proto-cultivation practice led to unintended consequences given that wild rice responds to drought stress owing to its phenotypic plasticity. Plant and panicle architectures were modified with transitions to more compact and erect tillers and to a closed panicle shape. They provide incentives to early foragers for intensifying their proto-cultivation practices and so could have also triggered initial cultivation of rice. They also triggered incipient domestication of rice, starting by the transition to selfing. According to this narrative, it is even possible that rice incipient domestication preceded cultivation.

Directional selection at gene expression level contributes to the speciation of Asian rice cultivars

Differences in expression levels play important roles in phenotypic variation across species, especially those closely related species with limited genomic differences. Therefore, studying gene evolution at expression level is important for illustrating phenotypic differentiation between species, such as the two Asian rice cultivars, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. In this study, we evaluated the gene expression variation at inter-subspecies and intra-subspecies levels using transcriptome data from seedlings of three indica and japonica rice and defined four groups of genes under different natural selections. We found a substantial of genes (about 79%) that are under stabilizing selection at the expression level in both subspecies, while about 16% of genes are under directional selection. Genes under directional selection have higher expression level and lower expression variation than those under stabilizing selection, which suggest a potential explanation to subspecies adaptation to different environments and interspecific phenotypic differences. Subsequent functional enrichment analysis of genes under directional selection shows that indica rice have experienced the adaptation to environmental stresses, and also show differences in biosynthesis and metabolism pathways. Our study provides an avenue of investigating indica-japonica differentiation through gene expression variation, which may guide to rice breeding and yield improvement.

DRY RICE HUSK FILLER EFFECT TO TENSILE BEHAVIORS OF RECYCLED HIGH-DENSITY POLYETHYLENE (HDPE)-BASED GREEN COMPOSITES

The possibility of using plastic waste to manufacture hybrid bio-composite materials with the dry husk of Asian rice (Oryza sativa L.) is investigated. The most polluted and unsustainable plastic waste is High-Density Polyethylene (HDPE) due to its single-use, which decreases in quality if it is reused is selected. The mixtures chosen are local natural fiber and easy to find, potentially a preliminary study of a composites building material. Furthermore, to improve the tensile properties of this hybrid bio-composite material, an additional organic filler is used, such as rice husk (Oryza sativa L.) in a combination of 10%, 12%, and 15%. Samples for this study were processed using the hot press methods based on ASTM D882. Tested for tensile strength, modulus young, yield stress, and elongation is carried out to see an increase in the performance of the biocomposite material. The test results show that the best tensile properties are samples with 12% rice husk, resulting in excellent sample compatibility proofed by Scan Electron Microscopy to study bio-morphological composites. This project has shown that the composites based on natural fiber will be potential building materials due to their improved tensile properties.