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Background and aims: The accumulation of soil organic carbon (SOC) is a crucial process in mitigating climate change and ensuring soil quality. Subtropical plantations in China have shown high potential for enhancing SOC sequestration due to their high carbon sink capacity. However, the dynamics and compositions of SOC after long term afforestation are still poorly understood. Methods: We examined the dynamics of SOC and its fractions of different soil layers (0–5 cm, 5–10 cm, 10–20 cm, 20–40 cm, 40–80 cm, 80–100 cm) in a mixed broadleaf-conifer plantation (BCP), a Masson pine plantation (MP), and a Slash pine plantation (SP), and an enclosed forest (EF) in subtropical China. Both physical fractions (particulate organic carbon (POC), soil clay organic carbon (SOCclay), soil silt organic carbon (SOCsilt)) and chemical fractions (iron-aluminum-bound organic carbon (Fe/Al-OC), and calcium-bound organic carbon (Ca-OC)) were determined. Additionally, soil physicochemical properties were further analyzed. Results: Our results showed the SOC storage in the EF, BCP, MP, and SP in 2019 increased by 82%, 238%, 126%, and 103% respectively compared to 1984. The proportions of MAOC to SOC were respectively as follows: SP (65.9%) > BCP (64.9%) > EF (61.6%) > MP (53.9%). The mean proportions of SOCclay to MAOC were as follows: BCP (71.1%) > EF (66.9%) > MP (58.5%) > SP (51.0%). The mean proportions of Fe/Al-OC to MAOC were as follows: EF (53.3%) > SP (48.3%) > MP (47.9%) > BCP (39.8%). All these proportion increased with soil depth. RDA and PLS-SEM analysis revealed that soil nitrogen content and electrochemical properties (pH and EC) were the main factors that controlled SOC content and fractions. Conclusions: Subtropical plantations have significant soil carbon sequestration capabilities, but they are currently nearing saturation. Soil nitrogen content may be key factor limiting further enhancement of carbon sequestration. Due to the high proportion of MAOC and relative consistent SOC storage, BCP and SP are recommended as priorities for plantation regeneration in subtropical China. [ABSTRACT FROM AUTHOR]

Summary: MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA‐seq analysis, combined with in situ hybridization assay revealed that up‐regulation of two miR528 targets coding for Cu/Zn‐SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528‐SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528‐SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation‐mediated crop improvement. [ABSTRACT FROM AUTHOR]

Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management. Root-associated microbiomes contribute to plant growth and health. Here, the authors unveil the quantitative development of the root microbiome under unbalanced fertilization and highlight a key microbial cluster for soybean productivity. [ABSTRACT FROM AUTHOR]

Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils. [ABSTRACT FROM AUTHOR]

The lack of genome editing platforms has hampered efforts to study and improve forage crops that can be grown on lands not suited to other crops. Here, we established efficient Agrobacterium‐mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR‐associated nuclease 9 (Cas9) genome editing in a perennial, stress‐tolerant forage grass, sheepgrass (Leymus chinensis). By screening for active single‐guide RNAs (sgRNAs), accessions that regenerate well, suitable Agrobacterium strains, and optimal culture media, and co‐expressing the morphogenic factor TaWOX5, we achieved 11% transformation and 5.83% editing efficiency in sheepgrass. Knocking out Teosinte Branched1 (TB1) significantly increased tiller number and biomass. This study opens avenues for studying gene function and breeding in sheepgrass. [ABSTRACT FROM AUTHOR]

Phased small interfering RNAs (phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice (Oryza sativa) low temperature-induced Argonaute (AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis; it also binds 21-nt phasiRNAs with a 5′ terminal U. In total, phasiRNAs from 972 loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature. [ABSTRACT FROM AUTHOR]

Summary: Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown.Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss‐function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature.We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre‐rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre‐rRNAs are observed in ospus1‐1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1‐1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress‐responsive state, preventing excess reactive oxygen species accumulation.Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement. [ABSTRACT FROM AUTHOR]

SUMMARY: In rice (Oryza sativa), the lemma and palea protect the internal organs of the floret，provide nutrients for seed development, and determine grain size. We previously revealed that a trans‐acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR‐ARF) regulates lemma polarity establishment via post‐transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR‐ARF formation requires RNA‐DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR‐ARF–ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6‐1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping‐by‐sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6‐1 lemma defect but not the defect in tasiR‐ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1‐associated sites, most of which contain the SPBP‐box binding motif (RGAATAWW) and are located in the promoter, protein‐coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR‐ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR‐ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development. Significance Statement: The lemma and palea are unique and important organs for rice, providing nutrients and protection for floret and seed development, and directly affecting grain size. Our findings show that the expression of OsARF3a was controlled by both OsKANADI1 and via RDR6 at the transcription and post‐transcription levels, thus ensuring the normal development of glumes in rice. [ABSTRACT FROM AUTHOR]

Marginal land refers to the land with low agricultural productivity and economic benefit and fragile ecology due to the prominent limitation of soil barrier, strong restriction of water and heat resources as well as harsh topographic conditions. In China, the existing marginal land is about 1.17 billion mu (15 mu is equal to 1 ha), which is the most important resource of strategic emergency to deal with the cultivated land gap of 700 million mu. Marginal land storage is a major strategy for national food security. It has become a new international research trend to increase the productivity and ecological functions of marginal land by modulating the interaction between plant and soil microbial. This includes breeding high stress-tolerant plants, screening and application of plant growth promotion rhizobacteria (PGPR) to promote plant growth on marginal land, and strengthening soil microbial functions to improve soil quality and health. In view of the marginal land productivity expansion and ecological benefit improvement, it is necessary to formulate the overall action plans based on the principles of ecological priority and green development. We should carry out the marginal land R & D project with the idea of "plant first, soil-improvement as the base, water security, microbial control, and the integration of plant-soil-microbial ecological system". (1) We should build a national database of marginal land and formulate the protection and management zoning plan. (2) We should develop four aspects of basic theory research namely, stress-tolerant plants breeding and its adaptive mechanism, efficient utilization of water and fertilize, soil obstacle factor reduction and biological networks induction/acclimatization, and the interaction between plant and microbial. (3) Focusing on coastal saline-alkali land in north and east China, soda alkali-saline land in northeast China, saline-alkali land in northwest inland, yellow spongy soils slope on the loess plateau, red soil and purple soil slope land in south hilly region, we should build different types of ecological farmland by integrating various technologies and theories. This will promote the protection and sustainable utilization of marginal land resources, and support the timely launch of the efficient use of contiguous marginal land to achieve the goal of increasing productivity by adding 700 million mu of medium-high grade arable land. This will be also helpful to ensure the implementation of the strategy of "storing grain in land and technology" and rural vitalization, and the construction of ecological civilization in China's ecologically fragile areas. [ABSTRACT FROM AUTHOR]

In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored. However, the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves; at the post-transcriptional level, aging also modulated miR528 levels by enhancing pri-miR528 alternative splicing. We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties, which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528. Taken together, our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants. This study reveals the mechanisms that fine-tune miR528 accumulation both transcriptionally and post-transcriptionally through the circadian clock, aging, and natural variations. miR528 plays a role in promoting rice flowering under long-day conditions by targeting OsRFI2. The transcription factor OsSPL9 directly binds the MIR528 promoter, activates MIR528 transcription, and potentially differentiates miR528 levels among rice varieties. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are 20–24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant–environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research. [ABSTRACT FROM AUTHOR]

Phytolith-occluded organic carbon (PhytOC) is considered one of the most promising terrestrial carbon (C) sinks. Different methods are used for phytolith extraction from wet-ashing techniques and the subsequent determination of PhytOC content from soil. This is in order to optimize the wet-ashing techniques and to improve estimation accuracy of C sequestration potential of phytoliths from soil. Results show that the organic matter removal and carbonate removal protocol, applying sonication, has a significant effect on phytolith extraction. Namely, the sequential removal of first organic matter and then carbonates applied to such methods could eliminate greater than 17.14, 46.68, and 26.17% extraneous material compared to other methods. Moreover, phytoliths extracted using methods that apply sonication eliminated 7.49, 42.70, and 17.57% more extraneous material than methods that did not. Additionally, the procedure associated with the second oxidation step significantly influenced the determination of PhytOC content, that is, 29.34, 33.75, 26.41, and 64.64% of excess organic C were oxidized during this step. The upgraded optimal method we recommend for phytolith extraction in association with wet-ashing techniques and the subsequent determination of PhytOC content is therefore to first apply sonication, then the second oxidation step, and finally the removal of organic matter. Using this optimal upgraded method, we estimated the C sequestration potential of phytoliths from the soil of slash pine in China at 0.51 Mt. C. Furthermore, using this upgraded optimal method increased the precision of the carbon sequestration potential of phytoliths from soil by up to 63.83%. [ABSTRACT FROM AUTHOR]

In karst areas, rock dissolution often results in the development of underground networks, which act as subterranean pathways for rapid water and nutrient (and possibly soil) loss during precipitation events. Loss of soluble nutrients degrades surface soils and decreases net primary productivity, so it is important to establish flow pathways and quantify nutrient loss during rainfall events of different magnitudes. We conducted a simulated rainfall experiment in karst and nonkarst areas to compare the concentration of nutrients in surface and subsurface flow water and effects on soil alkalinity in three lithologic soil formations under five different rainfall intensity treatments. Compared with the nonkarst area, the runoff in subsurface flows and the proportion of nutrient loss in the subsurface flow are larger in the karst area and less affected by rain intensity. The maximum loss loads of calcium (Ca2+) and magnesium (Mg2+) ions were 32.9 and 19.8 kg ha−1, respectively. With the estimate of base cation loss loads in the China southern karst area under the rainfall intensity of 45 mm h−1, more than 80% of the base cation loss load occurred in the limestone karst area. Although the alkalinity leaching value in nonkarst was similar to that in the karst area under simulated rainfall conditions, its impact on the ecological environment was quite different. [ABSTRACT FROM AUTHOR]

Karst topography covers more than 1/3 of the People's Republic of China in area. The porous, fissured, and soluble nature of the underlying karst bedrock (primarily dolomite and limestone) leads to the formation of underground drainage systems. Karst conduit networks dominate this system, and rainfall takes a crucial role on water cycle at China karst area. Nitrogen loss from the karst system is of particular concern, with regard to nutrient use efficiency as well as water quality, as much of the karst system, including steeply sloping terrain, is used for intensive agriculture. We use simulated rainfall experiments to determine the relationship between rainfall and nitrogen loss at typical karst slope land and then estimate nitrogen loss from the karst soil. The results show that both surface runoff and subsurface runoff have a significant linear correlation with rainfall at all studied sites. Subsurface runoff is larger than surface runoff at two karst sites, while the opposite is true at the non-karst site. Exponential function satisfactorily described the correlation between rainfall and nitrogen concentrations in runoff. Nitrates accounted for 60%-95% of the dissolved nitrogen loss (DN, an index of N-loss in this research). The estimated annual N-loss load varies between 1.05 and 1.67 Tg N/year in the whole karst regions of China from 1961 to 2014. Approximately, 90% of the N-loss load occurred during the wet season, and 90% of that passed through the subsurface. Understanding the processes and estimating N-loss is highly valuable in determining long-term soil security and sustainability in karst regions. [ABSTRACT FROM AUTHOR]

The karst critical zone is an essential component of the carbon (C) pool, constituting the global C cycle. It is referred to as one of the 'residual land sink' that remains largely indeterminate. Karst area (2.2×10 km) comprises 15% of the world's land area, and karst area comprises 3.44×10 km of area in China. Due to the complexity of karst structure and its considerable heterogeneity, C sequestration rate estimations contain large inaccuracies, especially in relation to the different methods used in calculations. Therefore, we reevaluated rock weathering-related C sink estimations in China (approximately 4.74 Tg C yr), which we calibrated from previous studies. Additionally, we stipulated that more comprehensive research on rock-soil-biology-atmosphere continuum C migration is essential to better understand C conversion mechanisms based on uncertainty analyses of C sink estimations. Moreover, we stressed that a collective confirmation of chemical methods and simulated models through a combined research effort could at least partially eliminate such uncertainty. Furthermore, integrated C cycling research need a long-term observation of the carbon flux of multi-interfaces. The enhanced capacity of ecosystem C and soil C pools remains an effective way of increasing C sink. Karst ecosystem health and security is crucial to human social development, accordingly, it is critical that we understand thresholds or potential C sink capacities in karst critical zones now and in the future. [ABSTRACT FROM AUTHOR]

Epigenetic gene variants, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Here, we identify a natural epiallele of OsAK1, which encodes a rice adenylate kinase. The Epi-ak1 plants show albino in young leaf and panicle with abnormal chloroplast structures. We found that no nucleotide sequence variation but hypermethylation at promoter region caused silencing of OsAK1 ( Os08g01770) in Epi-ak1 plants. OsAK1 localizes to chloroplast and many genes associated with photosynthesis processes were downregulated in Epi-ak1. Thus, the work identified a novel rice epiallele caused by DNA methylation changes, shedding light on significant roles of DNA methylation on rice development. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) play key regulatory roles in numerous developmental and physiological processes in animals and plants. The elaborate mechanism of miRNA biogenesis involves transcription and multiple processing steps. Here, we report the identification of a pair of evolutionarily conserved NOT2_3_5 domain–containing-proteins, NOT2a and NOT2b (previously known as At-Negative on TATA less2 [NOT2] and VIRE2-INTERACTING PROTEIN2, respectively), as components involved in Arabidopsis thaliana   miRNA biogenesis. NOT2 was identified by its interaction with the Piwi/Ago/Zwille domain of DICER-LIKE1 (DCL1), an interaction that is conserved between rice (Oryza sativa) and Arabidopsis thaliana. Inactivation of both NOT2 genes in Arabidopsis caused severe defects in male gametophytes, and weak lines show pleiotropic defects reminiscent of miRNA pathway mutants. Impairment of NOT2s decreases the accumulation of primary miRNAs and mature miRNAs and affects DCL1 but not HYPONASTIC LEAVES1 (HYL1) localization in vivo. In addition, NOT2b protein interacts with polymerase II and other miRNA processing factors, including two cap binding proteins, CBP80/ABH1, CBP20, and SERRATE (SE). Finally, we found that the mRNA levels of some protein coding genes were also affected. Therefore, these results suggest that NOT2 proteins act as general factors to promote the transcription of protein coding as well as miRNA genes and facilitate efficient DCL1 recruitment in miRNA biogenesis. [ABSTRACT FROM AUTHOR]

Higher plants have evolved multiple RNA-dependent RNA polymerases (RDRs), which work with Dicer-like (DCL) proteins to produce different classes of small RNAs with specialized molecular functions. Here we report that OsRDR6, the rice ( Oryza sativa L.) homolog of Arabidopsis RDR6, acts in the biogenesis of various types and sizes of small RNAs. We isolated a rice osrdr6-1 mutant, which was temperature sensitive and showed spikelet defects. This mutant displays reduced accumulation of tasiR-ARFs, the conserved trans-acting siRNAs (tasiRNAs) derived from the TAS3 locus, and ectopic expression of tasiR-ARF target genes, the Auxin Response Factors (including ARF2 and ARF3/ETTIN). The loss of tasiR-mediated repression of ARFs in osrdr6- 1 can explain its morphological defects, as expression of two non-targeted ARF3 gene constructs ( ARF3muts) in a wild-type background mimics the osrdr6 and osdcl4- 1 mutant phenotypes. Small RNA high-throughput sequencing also reveals that besides tasiRNAs, 21-nucleotide (nt) phased small RNAs are also largely dependent on OsRDR6. Unexpectedly, we found that osrdr6- 1 has a strong impact on the accumulation of 24-nt phased small RNAs, but not on unphased ones. Our work uncovers the key roles of OsRDR6 in small RNA biogenesis and directly illustrates the crucial functions of tasiR-ARFs in rice development. [ABSTRACT FROM AUTHOR]

Summary Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice ( Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer-Like (DCL) family, including OsDCL1, -3a, -3b and -4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4-1, we revealed that the processing of 21-nucleotide siRNAs, including trans-acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24-nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase-mediated 5′ rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21- and 24-nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA (sRNA) targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice ( Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93–11 ( Oryza sativa L. ssp. indica). One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORs ( ARFs) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligasemediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. [ABSTRACT FROM AUTHOR]

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties. [ABSTRACT FROM AUTHOR]

Phytoplankton community characteristics and associative primary productivity, which reflect the ecological and nutritional status of water, are sensitive to environmental change. Particularly, nutrient inputs have a significant effect on phytoplankton growth and development as well as the biogeochemical cycle of watersheds. We investigated the phytoplankton community and nutrient status downstream from the Gan River into Poyang Lake. On a catchment scale, the phytoplankton communities and associative primary productivity from these two water bodies differed. The Poyang Lake phytoplankton community is composed of seven phyla of algae, whereas the Gan River is composed of six, the dominant phyla of phytoplankton being Bacillariophyta and Cryptophyta in Poyang Lake and Gan River, respectively. Phytoplankton abundance and primary productivity were significantly higher in Poyang Lake. Lower nitrogen (N) and phosphorous (P) concentrations and higher carbon (C) and silicon (Si) concentrations significantly affected the phytoplankton communities and primary productivity distribution in the entire Poyang Lake Basin. In this regard, we found a significant correlation between the phytoplankton community of the Gan River and P and N, whereas N and Si primarily regulated the phytoplankton community structure of Poyang Lake. Moreover, we found a significant correlation between DTN, Si/P, DIC/P, and primary productivity in the Gan River, whereas NH4+ jointly controlled primary productivity in Poyang Lake. Furthermore, the Margalef Richness Index (0.84–2.41) can be indicative of the environmental water quality status; and we determined that the most area of Poyang Lake and Gan River both were P restriction and moderately polluted, whereas the entrance of the Gan River into Poyang Lake was seriously polluted, which confirms that the Gan River is a main and crucial source of Poyang Lake pollution. Nanjishan Nature Reserve was already slightly eutrophic due to the high nutrient content and a large number of algae in the south‐east of Poyang Lake, but the Gan River had good river fluidity, so some areas of the Gan River were oligotrophic. [ABSTRACT FROM AUTHOR]

Vegetation cover and soil infiltration can result in nitrogen (N) redistribution and associative isotopic fractionation. This study investigated N and its isotopic characteristics from deposition to baseflow under different vegetation canopy cover types in a subtropical watershed in China. Results showed that canopy interception via vegetation cover types exhibited notable dilution effects on reactive nitrogen (Nr) deposition during the rainy season, with the highest maximum value of 287.4%. The range of δ15N changed from 3.0‰ to 11.9‰ in throughfall, which may have resulted from an increase in N taken up by vegetation and particles washed away from plant leaves during rainfall events. Throughfall, soil water, precipitation, and rainfall run‐off were the sources of D and 18O‐H2O in baseflow river water, wherein the rainwater and rainfall run‐off contributed 73% ± 8% and 15% ± 12%, respectively. Soil water was the main source of 15N‐NO3 in baseflow river water, which contributes 78% ± 4% of overall source, but precipitation only contributes 10%. The average annual Nr deposition flux was 24.4 ± 4.2 kg·ha−1·yr−1, whereas the annual total nitrogen exportation flux was 1062 ± 269.8 kg·yr−1. The 46% of HDO or D2O for river water came from rainfall run‐off, which would transport a maximum nitrate flux of 354 kg·yr−1. Moreover, vegetation cover and soil infiltration resulted in δ15N enrichment and a decrease in Nr in river flow. [ABSTRACT FROM AUTHOR]