Inorganic fertilizer use and its association with rice yield gaps in sub-Saharan Africa.

Where and which countries should receive higher priority for improving inorganic fertilizer use in rice fields in sub-Saharan Africa (SSA)? This study addressed this question by assessing the spatial variation in fertilizer use and its association with rice yield and yield gap in 24 SSA countries through a systematic literature review of peer-reviewed papers, theses, and grey literature published between 1995 and 2021. The results showed a large variation in N, P, and K fertilizer application rates and rice yield and an opportunity for narrowing the yield gap by increasing N and P rates, especially in irrigated rice systems. We identified clusters of sites/countries based on nutrient input and yield and suggested research and development strategies for improving yields and optimizing nutrient use efficiencies. Further research is essential to identify the factors causing low fertilizer use and the poor association between its use and yield in rainfed systems.

MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels.

Improving crop yield potential through an enhanced response to rising atmospheric CO2 levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO2 levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO2 enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO2 levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO2 levels.

In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency.

Tillering is an important trait in rice productivity. We introduced mutations into the coding region of rice TEOSINTE BRANCHED1 (OsTB1), which is a negative regulator of tillering, using CRISPR/Cas9. The frameshift mutants exhibited substantially enhanced tillering and produced 3.5 times more panicles than the non-mutated plants at maturity. This enhanced tillering resulted in increased spikelet number; however, grain yields did not increase due to substantially reduced filled grain rate and 1,000-grain weight. In contrast, in-frame mutations in OsTB1 had the effect of slightly increasing tiller numbers, and the in-frame mutants had 40% more panicles than non-mutated plants. The grain yield of in-frame mutants also did not increase on nutrient-rich soil; however, under phosphorus-deficient conditions, where tillering is constrained, the in-frame mutants gave a significantly higher grain yield than non-mutated plants due to higher spikelet number and maintained filled grain rate. Rice grassy tiller1 (OsGT1)/OsHox12, which is directly regulated by OsTB1 to suppress tillering, was moderately down-regulated in in-frame mutants, suggesting that OsTB1 with the in-frame mutation shows partial function of intact OsTB1 in regulating OsGT1/OsHox12. We propose that mildly enhanced tillering by in-frame mutation of OsTB1 can improve grain yield under low phosphorus conditions.

Deep Learning Enables Instant and Versatile Estimation of Rice Yield Using Ground-Based RGB Images.

Rice (Oryza sativa L.) is one of the most important cereals, which provides 20% of the world's food energy. However, its productivity is poorly assessed especially in the global South. Here, we provide a first study to perform a deep-learning-based approach for instantaneously estimating rice yield using red-green-blue images. During ripening stage and at harvest, over 22,000 digital images were captured vertically downward over the rice canopy from a distance of 0.8 to 0.9 m at 4,820 harvesting plots having the yield of 0.1 to 16.1 t·ha-1 across 6 countries in Africa and Japan. A convolutional neural network applied to these data at harvest predicted 68% variation in yield with a relative root mean square error of 0.22. The developed model successfully detected genotypic difference and impact of agronomic interventions on yield in the independent dataset. The model also demonstrated robustness against the images acquired at different shooting angles up to 30° from right angle, diverse light environments, and shooting date during late ripening stage. Even when the resolution of images was reduced (from 0.2 to 3.2 cm·pixel-1 of ground sampling distance), the model could predict 57% variation in yield, implying that this approach can be scaled by the use of unmanned aerial vehicles. Our work offers low-cost, hands-on, and rapid approach for high-throughput phenotyping and can lead to impact assessment of productivity-enhancing interventions, detection of fields where these are needed to sustainably increase crop production, and yield forecast at several weeks before harvesting.

Synergy between a shallow root system with a DRO1 homologue and localized P application improves P uptake of lowland rice.

Improved phosphorus (P) use efficiency for crop production is needed, given the depletion of phosphorus ore deposits, and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has been little understood. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots after placing P near the roots at transplanting (P-dipping). The experiment identified that the P-dipping created an available P hotspot at the plant base of the soil surface layer where the qsor1-NIL had the greatest root biomass and root surface area despite no genotyipic differences in total values, whereby the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The superior surface root development of qsor1-NIL could have facilitated P uptakes from the P hotspot, implying that P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.

Development and evaluation of pyramiding lines carrying early or late heading QTLs in the indica rice cultivar 'IR64'.

The heading date is an important trait for determining regional and climatic adaptability in rice. To expand the adaptability of the indica rice cultivar 'IR64', we pyramided multiple early or late heading quantitative trait locus (QTLs) in the 'IR64' genetic background by crossing previously developed near-isogenic lines (NILs) with a single QTL for early or late heading. The effects of pyramiding QTLs were observed in three different climatic zones of the Philippines, Madagascar, and Japan. The early heading pyramiding lines (PYLs) headed 6.2 to 12.8 days earlier than 'IR64' while the late heading PYLs headed 18.8 to 27.1 days later than 'IR64'. The PYLs tended to produce low grain yield compared to 'IR64'. The low yield was not improved by combining SPIKE, which is a QTL that increases the number of spikelets per panicle. Conversely, 'IR64-PYL(7+10)' carrying Hd5 and Hd1 headed earlier, produced more tillers, and more panicles per m2 than 'IR64', and mitigated the yield decrease in early heading. These results suggest that the effects of pyramided QTLs on heading date were consistent across various environments and PYLs could be used to enhance the adaptation of 'IR64' in other rice growing environments.

P-dipping of rice seedlings increases applied P use efficiency in high P-fixing soils.

Applied phosphorus (P) use efficiency is generally low due to the low mobility of P in soil and its affinity to form insoluble complexes. Localized P application nearby the root zone is a potential approach to overcome this issue in crop production. However, the interaction with soil conditions is little understood, which results in less effective application of this approach. Using root-box experiments and changing P-retention capacity of soils, we revealed that applied P use efficiency of rice can be substantially improved by dipping seedlings in P-enriched slurry at transplanting (P-dipping) even in highly P-fixing soils. Spatial analysis of soluble P in soils indicated that P-dipping creates a P hotspot because the P-enriched slurry is transferred with seedling roots. The P hotspot could have induced vigorous surface root and facilitated further P uptake from the spot. In contrast, the effect of conventional P incorporation depended on P-retention capacity of soils; no increases in soluble P content in soils or plant P uptakes were observed when P-retention capacity was high. Our finding of significant interaction between localized P application and a specific soil property should help improving applied P use efficiency and achieving sustainable rice production against depleting P fertilizer resources.