Moderate Soil Drying Research Articles

Transcriptomic and Hormonal Changes in Wheat Roots Enhance Growth under Moderate Soil Drying.

Understanding the mechanisms that regulate plant root growth under soil drying is an important challenge in root biology. We observed that moderate soil drying promotes wheat root growth. To understand whether metabolic and hormonic changes are involved in this regulation, we performed transcriptome sequencing on wheat roots under well-watered and moderate soil drying conditions. The genes upregulated in wheat roots under soil drying were mainly involved in starch and sucrose metabolism and benzoxazinoid biosynthesis. Various plant hormone-related genes were differentially expressed during soil drying. Quantification of the plant hormones under these conditions showed that the concentrations of abscisic acid (ABA), cis-zeatin (CZ), and indole-3-acetic acid (IAA) significantly increased during soil drying, whereas the concentrations of salicylic (SA), jasmonic (JA), and glycosylated salicylic (SAG) acids significantly decreased. Correlation analysis of total root length and phytohormones indicated that CZ, ABA, and IAA are positively associated with wheat root length. These results suggest that changes in metabolic pathways and plant hormones caused by moderate soil drying help wheat roots grow into deeper soil layers.

Suppressing spikelet degeneration increases grain yield under moderate soil drying during meiosis in rice

Spikelet degeneration is a critical physiological issue that limits grain yield in rice (Oryza sativa L.), influenced by soil moisture conditions during meiosis. The study aimed to investigate the role and mechanism of moderate soil drying in spikelet degeneration and grain yield, as well as to establish a strategy and irrigation regime for suppressing spikelet degeneration to increase grain yield in rice. Field experiments were conducted involving two irrigation regimes: conventional well-watered (C-WW) and moderate soil drying (M-SD) during meiosis. Transgenic rice lines and chemical regulators were employed to elucidate the underlying partial biological mechanisms of this process. The results showed that M-SD regime effectively reduced spikelet degeneration rate and increased grain yield compared to C-WW. This improvement under M-SD regime was primarily attributed to the enhanced proline and aquaporin-mediated osmotic balance and redox homeostasis in young rice panicles, as well as the increased root activity during meiosis. The increased levels of brassinosteroids (BRs) and decreased levels of ethylene (ETH) in young panicles under the M-SD were closely associated with the enhanced proline and aquaporin-mediated osmotic balance and redox homeostasis, decreased oxidative damage, and reduced spikelet degeneration rate. The intrinsic relationship among key aquaporin genes expression and proline levels, osmotic balance and redox homeostasis, spikelet degeneration rate, as well as BRs and ETH levels, was further confirmed through the use of transgenic rice lines and chemical regulators. Collectively, an M-SD regime during meiosis can effectively suppress spikelet degeneration and thereby enhance grain yield, primarily through well-maintained osmotic balance and redox homeostasis in rice.

Involvement of brassinosteroids and abscisic acid in spikelet degeneration in rice under soil drying during meiosis.

Spikelet degeneration in rice (Oryza sativa L.) is a serious physiological defect, and can be regulated by soil moisture status and phytohormones. This study investigated the possibility that brassinosteroids (BRs) in collaboration with abscisic acid (ABA) are involved in mediating the effect of soil drying during meiosis on spikelet degeneration in rice. Three rice cultivars were field grown and three irrigation regimes including well watered (WW), moderate soil drying (MD), and severe soil drying (SD) were imposed during meiosis. MD significantly decreased spikelet degeneration in comparison with WW, due mainly to the alleviation in oxidative damage via enhancing ascorbate-glutathione (AsA-GSH) cycle activity in young panicles, and SD exhibited the opposite effects. Enhanced AsA-GSH cycle strength, decreased oxidative stress, and spikelet degeneration rate were closely associated with the synergistically elevated BR and ABA levels in young panicles in MD. In contrast, low BR and excessive ABA levels led to an increase in spikelet degeneration in SD. The three cultivars exhibited the same tendencies. The intrinsic link among AsA-GSH cycle, oxidative stress, spikelet degeneration rate, and BR and ABA levels was further verified by using transgenic rice lines and chemical regulators. BRs or ABA play a unique role in regulating spikelet degeneration. Synergistically increased BR and ABA levels in MD could work together to strengthen AsA-GSH cycle activity, leading to a reduction in oxidative damage and spikelet degeneration. On the other hand, a severe imbalance between low BR and excessive ABA levels may have contributed to the opposite effects in SD.

Auxin-producing bacteria promote barley rhizosheath formation

The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.

Irrigation regimes modulate non-structural carbohydrate remobilization and improve grain filling in rice (Oryza sativa L.) by regulating starch metabolism

Recently developed ‘super’ rice cultivars with greater yield potentials often suffer from the problem of poor grain filling, especially in inferior spikelets. Here, we studied the activities of enzymes related to starch metabolism in rice stems and grains, and the microstructures related to carbohydrate accumulation and transportation to investigate the effects of different water regimes on grain filling. Two ‘super’ rice cultivars were grown under two irrigation regimes of well-watered (WW) and alternate wetting and moderate soil drying (AWMD). Compared with the WW treatment, the activities of ADP glucose pyrophosphorylase (AGPase), starch synthase (StSase) and starch branching enzyme (SBE), and the accumulation of non-structural carbohydrates (NSCs) in the stems before heading were significantly improved, and more starch granules were stored in the stems in the AWMD treatment. After heading, the activities of α-amylase, β-amylase, sucrose phosphate synthase (SPS) and sucrose synthase in the synthetic direction (SSs) were increased in the stems to promote the remobilization of NSCs for grain filling under AWMD. During grain filling, the enzymatic activities of sucrose synthase in the cleavage direction (SSc), AGPase, StSase and SBE in the inferior spikelets were increased, which promoted grain filling, especially for the inferior spikelets under AWMD. However, there were no significant differences in vascular microstructures. The grain yield and grain weight could be improved by 13.1 and 7.5%, respectively, by optimizing of the irrigation regime. We concluded that the low activities of key enzymes in carbon metabolism is the key limitation for the poor grain filling, as opposed to the vascular microstructures, and AWMD can increase the amount of NSC accumulation in the stems before heading, improve the utilization rate of NSCs after heading, and increase the grain filling, especially in the inferior spikelets, by altering the activities of key enzymes in carbon metabolism.

Deep-water uptake under drought improved due to locally increased root conductivity in maize, but not in faba bean.

Moderate soil drying can cause a strong decrease in the soil-root system conductance. The resulting impact on root water uptake depends on the spatial distribution of the altered conductance relatively to remaining soil water resources, which is largely unknown. Here, we analyzed the vertical distribution of conductance across root systems using a novel, noninvasive sensor technology on pot-grown faba bean and maize plants. Withholding water for 4 days strongly enhanced the vertical gradient in soil water potential. Therefore, roots in upper and deeper soil layers were affected differently: In drier, upper layers, root conductance decreased by 66%-72%, causing an amplification of the drop in leaf water potential. In wetter, deeper layers, root conductance increased in maize but not in faba bean. The consequently facilitated deep-water uptake in maize contributed up to 21% of total water uptake at the end of the measurement. Analysis of root length distributions with MRI indicated that the locally increased conductance was mainly caused by an increased intrinsic conductivity and not by additional root growth. Our findings show that plants can partly compensate for a reduced root conductance in upper, drier soil layers by locally increasing root conductivity in wetter layers, thereby improving deep-water uptake.

Moderate soil drying improves physiological performances and kernel yield of maize

AbstractWater shortage is a serious problem in crop production, and maize (Zea mays L.) is the largest grain crop worldwide. It would have great significance in increasing kernel yield and water use efficiency to establish a high‐yielding and water‐saving irrigation technology in maize. In this study, two high‐yielding maize varieties were used and two irrigation regimes composed of well‐watered (WW) and moderate soil drying (MD) were conducted. Physiological performances, kernel yield, and water use efficiency were investigated. Compared with WW, the MD increased kernel yield by 4.69–6.40%, reduced irrigation water by 26.5–33.3%, and improved irrigation water use efficiency by 43.1–59.3%. In terms of physiological performances, the MD enhanced the leaf superoxide dismutase (SOD) activity, decreased malondialdehyde (MDA) content, increased the leaf photosynthetic rate and the contents of indole‐3‐acetic acid (IAA), zeatin (Z) + zeatin riboside (ZR), gibberellin‐3 (GA3), and abscisic acid (ABA) in inferior kernels, promoted the remobilization of non‐structural carbohydrates (NSC) from stalks and sheaths to kernels, and improved the filling rate and weight of inferior kernels. Correlation analysis showed that IAA, Z + ZR, and ABA contents in kernels were significantly and positively correlated with the kernel filling rate. These results suggest that the moderate soil drying imposed during the whole growth period of maize can achieve the dual goal of increasing food production and saving water by improving physiological performance, especially regulating hormonal levels in the kernel.

Post-anthesis moderate soil-drying facilitates source-to-sink remobilization of nitrogen via redistributing cytokinins in rice

This study investigated if and how cytokinins would mediate the effect of post-anthesis soil-drying on source-to-sink remobilization of nitrogen (N) in rice. Field experiments were conducted with normal (NN) and high amount of N (HN) applications. Two irrigation regimes, well-watered (WW) and moderate soil-drying (MD), were imposed from 8 days after full heading until maturity. The results showed that N use efficiency (NUE) including internal N use efficiency, N partial factor productivity and N harvest index, was substantially increased in MD relative to in WW. The MD promoted the reallocation and transfer of N, free amino acids (FAAs) and trans-zeatin (Z) + trans-zeatin riboside (ZR) from the source organs (stems and leaves) to the sink organ (panicles). Activities of protein degradation enzymes including endopeptidase (EP) and aminopeptidase (AP) in stems and leaves, and expression levels of FAAs transporter genes in panicles were substantially increased in MD than in WW, and were closely associated with Z + ZR content there. Application of kinetin to stems and leaves significantly decreased the activities of EP and AP, resulting in more N retention in stems and leaves and lower N harvest index. Application of kinetin to panicles significantly increased the expression levels of FAAs transporter genes in panicles, leading to less N retention in stems and leaves and higher N harvest index. Such facilitation in source-to-sink remobilization of N induced by the MD was greater at HN than at NN. Collectively, a post-anthesis MD can enhance source-to-sink remobilization of N and synergistically increase grain yield and NUE via redistributing cytokinins (Z + ZR) in rice.

Alternate wetting and moderate soil drying could increase grain yields in both main and ratoon rice crops

AbstractAlternate wetting and drying irrigation is a widely used irrigation method for water‐savings and high‐yielding in rice (Oryza sativa L.) production; however, its effect on grain yield (GY) in the main and ratoon crops is unclear. With two rice cultivars as materials, the effects on GY in the main and ratoon crop of three irrigation regimes, that is, conventional flooding irrigation (CI), alternate wetting and moderate soil drying irrigation (WMD), and alternate wetting and severe soil drying irrigation (WSD), during grain filling of the main crop were investigated. Compared with CI, WMD increased GY by 6.0∼6.5% in the main crop by increasing the 1,000‐grain weight and filled grain rate, whereas the ratoon crop GY increased by 13.3∼14.6% via increased panicle number. The WSD had no significant effects on the main crop GY, but significantly decreased ratoon crop GY by decreasing panicle number. A higher leaf photosynthetic rate, leaf area index, root oxidation activity, dry matter accumulation and nonstructural carbohydrate (NSC) translocation under WMD primarily drove the increased 1,000‐grain weight and filled grain rate in the main crop. Under WMD, higher soluble sugar contents catalysed by high amylase activity and higher zeatin + zeatin riboside in stems of the main crop promoted the growth of regenerated buds and increased the ratoon crop panicle number. In conclusion, WMD during grain filling of the main crop improved the growth and development of the main crop and promote the germination of regenerated buds, thereby increasing the GY of both main and ratoon crops.

Moderate Soil Drying-Induced Alternative Splicing Provides a Potential Novel Approach for the Regulation of Grain Filling in Rice Inferior Spikelets.

Poor grain filling of inferior spikelets, especially in some large-panicle rice varieties, is becoming a major limitation in breaking the ceiling of rice production. In our previous studies, we proved that post-anthesis moderate soil drying (MD) was an effective way to promote starch synthesis and inferior grain filling. As one of the most important regulatory processes in response to environmental cues and at different developmental stages, the function of alternative splicing (AS) has not yet been revealed in regulating grain filling under MD conditions. In this study, AS events at the most active grain-filling stage were identified in inferior spikelets under well-watered control (CK) and MD treatments. Of 16,089 AS events, 1840 AS events involving 1392 genes occurred differentially between the CK and MD treatments, many of which function on spliceosome, ncRNA metabolic process, starch, and sucrose metabolism, and other functions. Some of the splicing factors and starch synthesis-related genes, such as SR protein, hnRNP protein, OsAGPL2, OsAPS2, OsSSIVa, OsSSIVb, OsGBSSII, and OsISA1 showed differential AS changes under MD treatment. The expression of miR439f and miR444b was reduced due to an AS event which occurred in the intron where miRNAs were located in the MD-treated inferior spikelets. On the contrary, OsAGPL2, an AGPase encoding gene, was alternatively spliced, resulting in different transcripts with or without the miR393b binding site, suggesting a potential mechanism for miRNA-mediated gene regulation on grain filling of inferior spikelets in response to MD treatment. This study provides some new insights into the function of AS on the MD-promoted grain filling of inferior spikelets, and potential application in agriculture to increase rice yields by genetic approaches.

Synergistic interaction between ABA and IAA due to moderate soil drying promotes grain filling of inferior spikelets in rice.

Poor grain filling of inferior spikelets is becoming a severe problem in some super rice varieties with large panicles. Moderate soil drying (MD) after pollination has been proven to be a practical strategy to promote grain filling. However, the molecular mechanisms underlying this phenomenon remain largely unexplored. Here, transcriptomic analysis of the most active grain filling stage revealed that both starch metabolism and phytohormone signaling were significantly promoted by MD treatment, accompanied by increased enzyme activities of starch synthesis and elevated abscisic acid (ABA) and indole-3-acetic acid (IAA) content in the inferior spikelet. Moreover, the IAA biosynthesis genes OsYUC11 and OsTAR2 were upregulated, while OsIAA29 and OsIAA24, which encode two repressors of auxin signaling, were downregulated by MD, implying a regulation of both IAA biosynthesis and auxin signal transduction in the inferior spikelet by MD. A notable improvement in grain filling of the inferior spikelet was found in the aba8ox2 mutant, which is mutated in an ABA catabolism gene. In contrast, overexpression of OsABA8ox2 significantly reduced grain filling. Interestingly, not only the IAA content, but also the expression of IAA biosynthesis and auxin-responsive genes displayed a similar trend to that in the inferior spikelet under MD. In addition, several OsTPP genes were downregulated in the inferior spikelets of both MD/ABA-treated wild-type plants and the aba8ox2 mutant, resulting in lower trehalose content and higher levels of -6-phosphate (T6P), thereby increasing the expression of OsTAR2, a target of T6P. Taken together, our results suggest that the synergistic interaction of ABA-mediated accumulation of IAA promotes grain filling of inferior spikelets under MD.

Identification of microRNAs regulating grain filling of rice inferior spikelets in response to moderate soil drying post-anthesis

The grain filling of inferior spikelets is much less complete than that of superior spikelets in rice cultivars with large panicles and numerous spikelets and is promoted by moderate soil drying (MD) post-anthesis. A growing body of evidence has shown that microRNAs function in regulating grain development. However, little is known about the mechanism of microRNA control of grain filling of inferior spikelets in response to MD. In this study, grain filling of inferior spikelets was promoted by MD treatment in Nipponbare. Small-RNA profiling at the most active grain-filling stage was conducted in inferior spikelets under control (CK) and MD treatment. Of 521 known and 128 novel miRNAs, 38 known and 9 novel miRNAs were differentially expressed between the CK and MD treatments. Target genes of differentially expressed miRNAs were involved in multiple developmental and signaling pathways associated with catalytic activity, carbohydrate metabolism, and other functions. Both miR1861 and miR397 were upregulated by MD, leading to a decrease in OsSBDCP1 and OsLAC, two negative regulators of SSIIIa activity and BR signaling, respectively. In contrast, miR1432 abundance was reduced by MD, resulting in upregulation of OsACOT and thus an elevated content of both ABA and IAA. These results suggest that both starch synthesis and phytohormone biosynthesis are regulated by differentially expressed miRNAs in inferior spikelets in response to MD treatment. Our results suggest the molecular mechanisms by which miRNAs regulate grain filling in inferior spikelets of rice under moderate soil drying, providing potential application in agriculture to increase rice yields by genetic approaches.

Topography in tropical forests enhances growth and survival differences within and among species via water availability and biotic interactions

Abstract Topography is associated with variation in soil water, biogeochemical properties and climate, which drive diversity by filtering species and promoting niche differences. However, the potential for topography to promote fitness differences and diversity among tree species and populations remains poorly tested in tropical rainforests, especially at small spatial scales in everwet climates. We reciprocally transplanted tree seedlings between ridge and riparian sites and manipulated neighbour abundance and water availability to assess growth and survival differences both among species and between populations within species in response to changes in biotic interactions and soil water gradients associated with topographic heterogeneity. Seedling growth rates were higher on the ridge, but probability of survival was lower on the ridge than the riparian site. Topography also altered growth and survival responses to water availability such that seedlings in the inundated soils in the riparian site had the lowest growth and survival but increased rapidly with moderate soil drying. By contrast, growth and survival on the ridge were generally unresponsive to drying, although severe drought on the ridge reinforced differences among species in growth rates and probability of survival. The patterns of growth and survival within species did not provide evidence of local adaptation between seedlings from lowland and upslope origins. However, within species, topographic seed‐origin determined the response of seedling growth and survival to increasing neighbour abundance, indicative of divergent selective pressures between individuals growing in different topographic environments. Combined, these results suggest that topographic heterogeneity promotes tropical forest diversity both at the species level via environmental filtering due to water availability and at the population level via functional responses to the density of neighbouring vegetation. A free Plain Language Summary can be found within the Supporting Information of this article.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying.

Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.

Spikelet differentiation and degeneration in rice varieties with different panicle sizes

AbstractAn essential feature of modern high‐yielding rice varieties is the production of numerous spikelets, but the physiological mechanism underlying spikelet formation in these varieties remains unclear. In this study, we explored the characteristics of spikelet differentiation and degeneration and the relevant physiological characteristics of rice varieties with different panicle sizes. The regulatory effects of alternate wetting and moderate soil drying (AWMD) on spikelet formation were also measured. We determined that the high spikelet number per panicle and grain yields of large‐panicle rice varieties were primarily due to a higher number of differentiated and surviving secondary spikelets. Furthermore, shoot dry weight, plant nitrogen (N) uptake, plant N concentration, non‐structural carbohydrate (NSC) accumulation in stems, leaf area, and leaf photosynthetic rate from branch differentiation stage (BDS) to spikelet differentiation stage (SDS) were positively correlated with the number of differentiated secondary spikelets per panicle. Plant N concentration, NSC accumulation in stems, and leaf photosynthetic rate at pollen mother cell meiosis (PMC) were negatively correlated with the number of degenerated secondary spikelets. Finally, the number of differentiated secondary spikelets of Huaidao 5 (small panicle size) and Yongyou 2640 (large panicle size) varieties was promoted by 19.2% and 6.6%, and the number of degenerated secondary spikelets was reduced by 14.4% and 6.3%, respectively, under AWMD treatment compared to continuously flooded treatment. Prominent spikelet formation under AWMD resulted from the shoot dry weight, plant N uptake, plant N concentration, NSC accumulation in stems, leaf area, and leaf photosynthetic rate. Collectively, improvements in these key aboveground indices mentioned above during the BDS to SDS and the plant N concentration, NSC accumulation in stems, and leaf photosynthetic rate at the PMC stage would benefit spikelet formation by promoting differentiation and reducing degeneration of secondary spikelets, thereby enhancing yield of large‐panicle rice varieties.

Tolerance to low phosphorus was enhanced by an alternate wetting and drying regime in rice

AbstractPhosphorus (P) deficiency is a limiting factor for sustainable rice (Oryza sativa L.) production. However, little is known about how rice varieties that differ in tolerance to low P perform under water‐saving irrigation. In this study, we characterized the responses of two rice varieties, ZD88 that has a weak tolerance to low soil P and YJ2 that has a strong tolerance to low soil P to two irrigation regimes under both optimal P (NP, 46.9 mg/kg Olsen‐P) and low P (LP, 6.8 mg/kg Olsen‐P). The first irrigation regime involved continuous flooding (CF), while the second involved alternate wetting and moderate soil drying (AWD). The study was conducted in plants grown in pot over two years. YJ2 exhibited stronger tolerance to LP than ZD88 under both irrigation regimes. Compared to CF, plants grown with AWD produced higher grain yields and had increased phosphorus translocation efficiencies, as well as higher metabolic phosphorus efficiencies and increased phosphorus harvest index values. The water use efficiencies of the two rice varieties were increased under both NP and LP under AWD conditions. The AWD regime also resulted in higher shoot dry weights and increased photosynthesis rates under LP compared with CF. Moreover, the remobilization of non‐structural carbohydrates from stems to the grain was also increased under the AWD regime, together with higher activities of sucrose‐phosphate synthase, sucrose synthase and peroxidases and increased abscisic acid contents in grains. Root dry weights and root to shoot ratios were also increased under AWD conditions, together with increased root acid phosphatase activities. Taken together, these results demonstrate that the AWD regime benefits rice production under LP environment.

Proteomic analysis reveals a role of ADP-glucose pyrophosphorylase in the asynchronous filling of rice superior and inferior spikelets

The poor grain filling of inferior spikelets (IS) situated on the lower secondary rachis branch leads to a remarkable decrease in rice yield and quality. The AGPase small subunit 2 (AGPS2) encodes a small subunit of adenosine diphosphate-glucose pyrophosphorylase (AGPase) enzyme, which plays an important role in sucrose-starch conversion and starch biosynthesis in the grain filling of rice. In the present study, qPCR analysis showed low expression abundance of AGPS2 in IS, compared to the superior spikelets (SS), which was consistent with the lower grain weight of IS. To evaluate the molecular mechanism of AGPS2, we first identified the AGPS2 interaction network through Co-immunoprecipitation (Co-IP). In total, 29 proteins of AGPS2 interaction network were characterized by LC–MS/MS. Bioinformatics analysis revealed that, the characterized proteins in the interaction network are likely to be related to starch synthesis, sugar conversion, energy pathway, and folding/modification, and most of them were involved in the grain filling of rice. The sequent Co-IP analysis showed that AGPS2 can bind to starch branching enzyme (SBE), pullulanase (PUL) and starch debranching enzyme (DBE) and assemble into starch synthesizing protein complex (SSPC). In addition, the 14-3-3 protein GF14e was also found to interact with AGPS2. Further analysis by qPCR showed that the expression of GF14e was much higher on IS than on SS. The qPCR results also showed that the expression of GF14e was relatively stable in SS, but changed significantly in IS under alternate wetting and moderate soil drying (WMD), which is consistent with the AGPS2 expression pattern. Our present work provides direct molecular evidence for the different expression patterns of AGPS2 in SS and IS, which could be greatly helpful for the molecular amelioration of the poor grain filling of IS in rice.

Comprehensive epigenome and transcriptome analysis of carbon reserve remobilization in indica and japonica rice stems under moderate soil drying.

Moderate soil drying (MD) imposed at the post-anthesis stage significantly improves carbon reserve remobilization in rice stems, increasing grain yield. However, the methylome and transcriptome profiles of carbon reserve remobilization under MD are obscure in indica and japonica rice stems. Here, we generated whole-genome single-base resolution maps of the DNA methylome in indica and japonica rice stems. DNA methylation levels were higher in indica than in japonica and positively correlated with genome size. MD treatment had a weak impact on the changes in methylation levels in indica. Moreover, the number of differentially methylated regions was much lower in indica, indicating the existence of cultivar-specific methylation patterns in response to MD during grain filling. The gene encoding β-glucosidase 1, involved in the starch degradation process, was hypomethylated and up-regulated in indica, resulting in improved starch to sucrose conversion under MD treatment. Additionally, increased expression of MYBS1 transactivated the expression of AMYC2/OsAMY2A in both indica and japonica, leading to enhanced starch degradation under MD. In contrast, down-regulated expression of MYB30 resulted in increased expression of BMY5 in both cultivars. Our findings decode the dynamics of DNA methylation in indica and japonica rice stems and propose candidate genes for improving carbon reserve remobilization.

Carbohydrate, hormone and enzyme regulations of rice grain filling under post-anthesis soil drying

In rice, the utilization of the carbon reserve pre-stored in rice contributes significantly to its yield. The initiation of whole-plant senescence is required to remobilise carbon reserve, pre-stored in the stem, to the grains. Controlled moderate soil-drying during the rice grain filling period has been shown to induce senescence, and hence, increase the remobilisation of non-structural carbohydrates from the stem to the grains. Nonetheless, the mechanism by which controlled moderate soil drying improves this carbon reserve remobilisation remains unclear. Functional transcriptomic and proteomic analyses of rice stems and grains under moderate soil drying conditions have provided molecular and genetic evidences to explain the effects of moderate soil drying at the grain filling stage. Enzyme activities involved in the starch degradation and sugar synthesis process in the stem, as well as the starch synthesis process in the grain, has been reported to be enhanced by moderate soil drying. Moreover, plant hormones, especially those with an increased ratio of abscisic acid to ethylene, promote the transportation of carbohydrate from the stem to the grains, with a concurrent increase in the activities of enzymes involved in the sugar metabolism process in both the stem and the grains. The understanding of the remobilisation of non-structural carbohydrates in genome-wide and physiological levels has increased, and some links between molecular clues and physiological responses have been proposed. However, a deeper comprehension of the molecular mechanisms underlying how soil drying enhances carbon reserve remobilisation is still necessary. In this review, we discuss the recent progress in the knowledge of non-structural carbohydrate remobilisation in rice stems under soil drying conditions after anthesis.

Analysis of Global Methylome and Gene Expression during Carbon Reserve Mobilization in Stems under Soil Drying.

In rice (Oryza sativa), a specific temporary source organ, the stem, is important for grain filling, and moderate soil drying (MD) enhanced carbon reserve flow from stems to increase grain yield. The dynamics and biological relevance of DNA methylation in carbon reserve remobilization during grain filling are unknown. Here, we generated whole-genome single-base resolution maps of the DNA methylome in the stem. During grain filling under MD, we observed an increase in DNA methylation of total cytosines, with more hypomethylated than hypermethylated regions. Genes responsible for DNA methylation and demethylation were up-regulated, suggesting that DNA methylation changes in the stem were regulated by antagonism between DNA methylation and demethylation activity. In addition, methylation in the CG and CHG contexts was negatively associated with gene expression, while that in the CHH context was positively associated with gene expression. A hypermethylated/up-regulated transcription factor of MYBS2 inhibited MYB30 expression and possibly enhanced β-Amylase5 expression, promoting subsequent starch degradation in rice stems under MD treatment. In addition, a hypermethylated/down-regulated transcription factor of ERF24 was predicted to interact with, and thereby decrease the expression of, abscisic acid 8'-hydroxylase1, thus increasing abscisic acid concentration under MD treatment. Our findings provide insight into the DNA methylation dynamics in carbon reserve remobilization of rice stems, demonstrate that MD increased this remobilization, and suggest a link between DNA methylation and gene expression in rice stems during grain filling.