Partially functional NARROW LEAF1 balances leaf photosynthesis and plant architecture for greater rice yield.

NARROW LEAF1 (NAL1) is an elite gene in rice (Oryza sativa), given its close connection to leaf photosynthesis, hybrid vigor, and yield-related agronomic traits; however, the underlying mechanism by which this gene affects these traits remains elusive. In this study, we systematically measured leaf photosynthetic parameters, leaf anatomical parameters, architectural parameters, and agronomic traits in indica cultivar 9311, in 9311 with the native NAL1 replaced by the Nipponbare NAL1 (9311-NIL), and in 9311 with the NAL1 fully mutated (9311-nal1). Leaf length, width, and spikelet number gradually increased from lowest to highest in 9311-nal1, 9311, and 9311-NIL. In contrast, the leaf photosynthetic rate on a leaf area basis, leaf thickness, and panicle number gradually decreased from highest to lowest in 9311-nal1, 9311, and 9311-NIL. RNA-seq analysis showed that NAL1 negatively regulates the expression of photosynthesis-related genes; NAL1 also influenced expression of many genes related to phytohormone signaling, as also shown by different leaf contents of 3-Indoleacetic acid, jasmonic acid, Gibberellin A3, and isopentenyladenine among these genotypes. Furthermore, field experiments with different planting densities showed that 9311 had a larger biomass and yield advantage under low planting density compared to either 9311-NIL or 9311-nall. This study shows both direct and indirect effects of NAL1 on leaf photosynthesis; furthermore, we show that a partially functional NAL1 allele helps maintain a balanced leaf photosynthesis and plant architecture for increased biomass and grain yield in the field.

Scheduling of nitrogen fertilizer topdressing during panicle differentiation to improve grain yield of rice with a long growth duration.

Topdressing at panicle differentiation (PF) according to soil fertility and regularity of rice nutrient absorption is an important agronomic practice used in cultivation of rice cultivars with a long growth duration. We studied the impacts of timing of nitrogen fertilizer application during PF on photosynthesis and yield-related agronomic traits in 'Y-Liang-You 900' and 'Y-Liang-You 6', which are representative rice cultivars with a long growth duration. Data for two years showed that timing of topdressing application during PF affected panicles per unit area, percentage grain set, spikelets per panicle, and leaf photosynthetic traits during the grain-filling period. Topdressing at the initial stage of flag-leaf extension resulted in higher grain yield (typically by 10.55-19.95%) than in plants without topdressing. Grain yield was significantly correlated with flag leaf photosynthetic rate and leaf SPAD value (r = 0.5640 and r = 0.5589, respectively; p < 0.01) at an advanced grain-filling stage (30 days after heading). Surprisingly, grain yield was not correlated with carbohydrate remobilization from the stem and sheath. For rice cultivars with a long growth duration, nitrogen-fertilizer topdressing must be applied at the initial stage of flag-leaf extension to delay leaf senescence during the grain-filling stage and realize the enhanced yield potential.

Architectural and Physiological Features to Gain High Yield in an Elite Rice Line YLY1.

Identification of traits strongly associated with high yield can help future gene engineering towards improvements of productivity. Here we systematically determine the major architectural and physiological features associated with high yield in two elite historical hybrid rice cultivars, i.e., YLY1 and LYP9. Data from a six-year experiment show that high yield of YLY1 are related to a number of architectural and physiological parameters. Compared to LYP9, YLY1 had 5.5% and 47.3% higher canopy photosynthesis under high and low photosynthetic photon flux densities, respectively, during the grain filling stage, an average 1.5% higher proportion of biomass allocation to above-ground tissues, a 4.5%-10.5% higher photosynthate reserve in leaf sheath before grain filling, and a more efficient photosynthate translocation during grain filling and finally an average 25.2% higher number of productive tillers. These features differ dramatically from features associated with high yield in YLY900 and Yongyou12#, two other high-yielding rice cultivars in China. These identified features and their combinations can support designing new strategies in the future high-yield rice breeding.

An in situ approach to characterizing photosynthetic gas exchange of rice panicle.

BACKGROUND: Photosynthesis of reproductive organs in C3 cereals is generally regarded as important to crop yield. Whereas, photosynthetic characteristics of reproductive organs are much less understood as compared to leaf photosynthesis, mainly due to methodological limitations. To date, many indirect methods have been developed to study photosynthesis of reproductive organs and its contribution to grain yield, such as organ shading, application of herbicides and photosynthetic measurement of excised organs or tissues, which might be intrusive and cause biases. Thus, a robust and in situ approach needs to be developed. RESULTS: Here we report the development of a custom-built panicle photosynthesis chamber (P-chamber), which can be connected to standard infrared gas analyzers to study photosynthetic/respiratory rate of a rice panicle. With the P-chamber, we measured panicle photosynthetic characteristics of seven high-yielding elite japonica, japonica-indica hybrid and indica rice cultivars. Results show that, (1) rice panicle is photosynthetically active during grain filling, and there are substantial inter-cultivar variations in panicle photosynthetic and respiratory rates, no matter on a whole panicle basis, on an area basis or on a single spikelet basis; (2) among the seven testing cultivars, whole-panicle gross photosynthetic rates are 17-54 nmol s-1 5 days after heading under photon flux density (PFD) of 2000 µmol (photons) m-2 s-1, which represent some 20-38% of that of the corresponding flag leaves; (3) rice panicle photosynthesis has higher apparent CO2 compensation point, light compensation point and apparent CO2 saturation point, as compared to that of a typical leaf; (4) there is a strong and significant positive correlation between gross photosynthetic rate 5 days after heading on a single spikelet basis and grain setting rate at harvest (Pearson correlation coefficient r = 0.93, p value < 0.0001). CONCLUSIONS: Rice panicle gross photosynthesis is significant, has great natural variation, and plays an underappreciated role in grain yield formation. The P-Chamber can be used as a tool to study in situ photosynthetic characteristics of irregular non-foliar plant organs, such as ears, culms, leaf sheaths, fruits and branches, which is a relatively less explored area in current cereal breeding community.

Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.).

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Ef-cd locus shortens rice maturity duration without yield penalty.

The contradiction between "high yielding" and "early maturing" hampers further improvement of annual rice yield. Here we report the positional cloning of a major maturity duration regulatory gene, Early flowering-completely dominant (Ef-cd), and demonstrate that natural variation in Ef-cd could be used to overcome the above contradictory. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition. Field test comparisons of early maturing Ef-cd near-isogenic lines with their wild types as well as of the derivative early maturing hybrids with their wild-type hybrids conducted under different latitudes determined that the early maturing Ef-cd allele shortens maturity duration (ranging from 7 to 20 d) without a concomitant yield penalty. Ef-cd facilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessing Ef-cd matured significantly earlier. Therefore, Ef-cd could be a vital contributor of elite early maturing hybrid varieties in balancing grain yield with maturity duration.

Systems models, phenomics and genomics: three pillars for developing high-yielding photosynthetically efficient crops.

Recent years witnessed a stagnation in yield enhancement in major staple crops, which leads plant biologists and breeders to focus on an urgent challenge to dramatically increase crop yield to meet the growing food demand. Systems models have started to show their capacity in guiding crops improvement for greater biomass and grain yield production. Here we argue that systems models, phenomics and genomics combined are three pillars for the future breeding for high-yielding photosynthetically efficient crops (HYPEC). Briefly, systems models can be used to guide identification of breeding targets for a particular cultivar and define optimal physiological and architectural parameters for a particular crop to achieve high yield under defined environments. Phenomics can support collection of architectural, physiological, biochemical and molecular parameters in a high-throughput manner, which can be used to support both model validation and model parameterization. Genomic techniques can be used to accelerate crop breeding by enabling more efficient mapping between genotypic and phenotypic variation, and guide genome engineering or editing for model-designed traits. In this paper, we elaborate on these roles and how they can work synergistically to support future HYPEC breeding.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow.

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

Quantitative descriptions of rice plant architecture and their application.

Plant architecture is an important agronomic trait, and improving plant architecture has attracted the attention of scientists for decades, particularly studies to create desirable plant architecture for high grain yields through breeding and culture practices. However, many important structural phenotypic traits still lack quantitative description and modeling on structural-functional relativity. This study defined new architecture indices (AIs) derived from the digitalized plant architecture using the virtual blade method. The influences of varieties and crop management on these indices and the influences of these indices on biomass accumulation were analyzed using field experiment data at two crop growth stages: early and late panicle initiation. The results indicated that the vertical architecture indices (LAI, PH, 90%-DRI, MDI, 90%-LI) were significantly influenced by variety, water, nitrogen management and the interaction of water and nitrogen, and compact architecture indices (H-CI, Q-CI, 90%-LI, 50%-LI) were significantly influenced by nitrogen management and the interaction of variety and water. Furthermore, there were certain trends in the influence of variety, water, and nitrogen management on AIs. Biomass accumulation has a positive linear correlation with vertical architecture indices and has a quadratic correlation with compact architecture indices, respectively. Furthermore, the combination of vertical and compact architecture indices is the indicator for evaluating the effects of plant architecture on biomass accumulation.