Light intensity-mediated auxin homeostasis in spikelets links carbohydrate metabolism enzymes with grain filling rate in rice.

Low light (LL) stress during the grain-filling stage acutely impairs the quality and quantity of starch accumulation in rice grains. Here, we observed that LL-induced poor starch biosynthesis is modulated by auxin homeostasis, which regulates the activities of major carbohydrate metabolism enzymes such as starch synthase (SS) and ADP-glucose pyrophosphorylase (AGPase) in rice. Further, during the grain-filling period under LL, the starch/sucrose ratio increased in leaves but significantly decreased in the developing spikelets. This suggests poor sucrose biosynthesis in leaves and starch in the grains of the rice under LL. A lower grain starch was found to be correlated with the depleted AGPase and SS activities in the developing rice grains under LL. Further, under LL, the endogenous auxin (IAA) level in the spikelets was found to be synchronized with the expression of a heteromeric G protein gene, RGB1. Interestingly, under LL, the expression of OsYUC11 was significantly downregulated, which subsequently resulted in reduced IAA in the developing rice spikelets, followed by poor activation of grain-filling enzymes. This resulted in lowered grain starch accumulation, grain weight, panicle number, spikelet fertility, and eventually grain yield, which was notably higher in the LL-susceptible (GR4, IR8) than in the LL-tolerant (Purnendu, Swarnaprabha) rice genotypes. Therefore, we hypothesize that depletion in auxin biosynthesis under LL stress is associated with the downregulation of RBG1, which discourages the expression and activities of grain-filling enzymes, resulting in lower starch production, panicle formation, and grain yield in rice.

Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice.

Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-novmiR5) and three known (osa-miR166c-3p, osa-miR2102-3p, and osa-miR530-3p) miRNAs were selected for their expression validation through miRNA-specific qRT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.

The role of phytochrome-mediated gibberellic acid signaling in the modulation of seed germination under low light stress in rice (O. sativa L.).

Seed germination plays cardinal roles in seedling establishment and their successive growth. However, seed germination is retarded by far-red (FR) enrichment under low light stress, and the inhibitory signalling mechanism remains ambiguous. Our results indicated that low light treatment, both in the open and growth chamber conditions, inhibits rice seed germination by decreasing the gibberellin (GA) contents. To explore the mechanism of GA-deficiency under low light stress, differential expression profiling of GA-anabolic, -catabolic, ABA -anabolic, -catabolic, and SLR1 was investigated, revealing that expression of ABA- anabolic, GA-catabolic genes and SLR1 was upregulated with a simultaneous downregulation of ABA-catabolic and GA-anabolic genes under low light treatment. These results suggested that FR-induced GA inadequacy is resulted by upregulation of SLR1 and GA-catabolism genes consequently increase DELLA that further subsided GA-responses in the germinating rice seeds. Moreover, we provided evidence that FR-induced GA inadequacy demotes rice seed germination by decreasing amylase activity, eventually decreasing the carbohydrate solubilization in the germinating seeds. Finally, we suggest that under low light stress, due to a retarded conversion of phytochrome A to their bioactive form, the ABA-catabolic genes were eventually upregulated with a simultaneous downregulation of GA-anabolic genes. Consequently, a lower GA pool fails to leverage the GA-dependent DELLA degradation, further shutting down the expected GA responses that reduce germination efficiency under FR-enriched light. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01167-7.

A chloroplast Glycolate catabolic pathway bypassing the endogenous photorespiratory cycle enhances photosynthesis, biomass and yield in rice (Oryza sativa L.).

Photorespiration accounts for 20-50 % reduction in grain yield in C3 crops. The process is essential to remove 2-phosphoglycolate produced due to the oxygenation activity of the ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) enzyme. Attempts were made to improve photosynthesis through enriched CO2 concentration by installing numerous photorespiratory bypass modules in the chloroplast of several crops. In this study, we have introduced Escherichia coli glycolate catabolic pathway (ECGC) into rice chloroplast to bypass photorespiration partially (PB) or completely (FB). Five genes encoding glyoxylate carboligase (GCL), tartronic semialdehyde reductase (TSR), and three subunits of glycolate dehydrogenase (GDH) were introduced to get FB plants, whereas only the three subunits of GDH were introduced to get PB plants. Southern analysis confirmed stable integration of the transgenes and their expression was confirmed by RT-qPCR analysis in the T3 progenies. Both FB and PB transformed lines exhibited increased photosynthetic efficiency, biomass, and grain yield than wild type (WT) with empty vector control. The introduction of ECGC pathway favoured the carboxylase activity of RuBisCO while decreasing its oxygenase activity fostering the functioning of Calvin-Benson cycle and resulting in an increased carbon-assimilation that was manifested in their superior architecture and harvest index. These findings will support rice and related cereal crop breeding programs to increase yield under elevated temperature and arid conditions.

Role of sedoheptulose-1,7 bisphosphatase in low light tolerance of rice (Oryza sativa L.).

Rice grain yield is drastically reduced under low light especially in kharif (wet) season due to cloudy weather during most part of crop growth. Therefore, 50-60% of yield penalty was observed. To overcome this problem, identification of low light tolerant rice genotypes with a high buffering capacity trait such as photosynthetic rate has to be developed. Sedoheptulose-1,7 bisphosphatase, a light-regulated enzyme, plays pivotal role in the Calvin cycle by regenerating the substrate (RuBP) for RuBisCo and therefore, indirectly regulates the influx of CO2 for this crucial process. We found a potential role of SBPase expression and activity in low light tolerant and susceptible rice genotypes by analyzing its influence on net photosynthetic rate and biomass. We observed a significant relationship of yield with photosynthesis, SBPase expression and activity especially under low light conditions. Two tolerant and two susceptible rice genotypes were used for the present study. Tolerant genotypes exhibited significant but least reduction compared to susceptible genotypes in the expression and activity of SBPase, which was also manifested in its photosynthetic rate and finally in the grain yield under low light. However, susceptible genotypes showed significant reduction in SBPase activity along with photosynthesis and grain yield suggesting that tracking the expression and activity of SBPase could form a simple and reliable method to identify the low light tolerant rice cultivars. The data were analyzed using the Indostat 7.5, Tukey-Kramer method through Microsoft Excel 2019 and PAST4.0 software. The significant association of SBPase activity with the grain yield, net assimilation rate, electron transfer rate, biomass and grain weight were observed under low light stress. These traits should be considered while selecting and breeding for low light tolerant cultivars. Thus, SBPase plays a major role in the low light tolerance mechanism in rice.

Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage.

Low light intensity is a great limitation for grain yield and quality in rice. However, yield is not significantly reduced in low light tolerant rice varieties. The work therefore planned for comparative transcriptome profiling under low light stress to decipher the genes involved and molecular mechanism of low light tolerance in rice. At active tillering stage, 50% low light exposure for 1 day, 3 days and 5 days were given to Swarnaprabha (low light tolerant) and IR8 (low light sensitive) rice varieties. Illumina (HiSeq) platform was used for transcriptome sequencing. A total of 6,652 and 12,042 genes were differentially expressed due to low light intensity in Swarnaprabha and IR8, respectively as compared to control. CAB, LRP, SBPase, MT15, TF PCL1 and Photosystem I & II complex related gene expressions were mostly increased in Swarnaprabha upon longer duration of low light exposure which was not found in IR8 as compared to control. Their expressions were validated by qRT-PCR. Overall study suggested that the maintenance of grain yield in the tolerant variety under low light might be results of accelerated expression of the genes which enable the plant to keep the photosynthetic processes moving at the same pace even under low light.

DNA as a digital information storage device: hope or hype?

The total digital information today amounts to 3.52 × 1022 bits globally, and at its consistent exponential rate of growth is expected to reach 3 × 1024 bits by 2040. Data storage density of silicon chips is limited, and magnetic tapes used to maintain large-scale permanent archives begin to deteriorate within 20 years. Since silicon has limited data storage ability and serious limitations, such as human health hazards and environmental pollution, researchers across the world are intently searching for an appropriate alternative. Deoxyribonucleic acid (DNA) is an appealing option for such a purpose due to its endurance, a higher degree of compaction, and similarity to the sequential code of 0's and 1's as found in a computer. This emerging field of DNA as means of data storage has the potential to transform science fiction into reality, wherein a device that can fit in our palms can accommodate the information of the entire world, as latest research has revealed that just four grams of DNA could store the annual global digital information. DNA has all the properties to supersede the conventional hard disk, as it is capable of retaining ten times more data, has a thousandfold storage density, and consumes 108 times less power to store a similar amount of data. Although DNA has an enormous potential as a data storage device of the future, multiple bottlenecks such as exorbitant costs, excruciatingly slow writing and reading mechanisms, and vulnerability to mutations or errors need to be resolved. In this review, we have critically analyzed the emergence of DNA as a molecular storage device for the future, its ability to address the future digital data crunch, potential challenges in achieving this objective, various current industrial initiatives, and major breakthroughs.