Effect of Removing Superior Spikelets on Grain Filling of Inferior Spikelets in Rice

Indole-3-Acetic Acid (IAA) and Sugar Mediate Endosperm Development in Rice (Oryza sativa L.)

The yield potential of large-panicle rice is often limited by grain-filling barriers caused by the development of inferior spikelets (IS). Photoassimilates, which are the main source of rice grain filling, mainly enter the caryopsis through the dorsal vascular bundle. The distribution of assimilates between superior spikelets (SS) and IS is influenced by auxin-mediated apical dominance; however, the mechanism involved is still unclear. In this study, the effect of auxin signaling on the grain filling of SS and IS was investigated in two large-panicle japonica rice varieties, W1844 and CJ03. Compared to SS, IS displayed delayed initiation of filling and a significantly lower grain weight. Furthermore, the endosperm development in IS remained stagnant at the coenocytic stage. The development of the dorsal vascular bundle in the IS was also slow, and poor sucrose-unloading was observed during the initial grain filling stage. However, the endosperm development in IS immediately started after the improvement of dorsal vascular bundle development. GUS activity staining further revealed that indole-3-acetic (IAA) was localized in the dorsal vascular bundle and surrounding areas, suggesting that the low IAA content observed in the IS during the initial grain filling stage may have delayed the development of the dorsal vascular bundle. Therefore, these results demonstrate that IAA may control sugar transport and unloading by regulating dorsal vascular bundle development, consequently affecting endosperm development in IS.

Overexpression of Orysa;KRP4 drastically reduces grain filling in rice

MAIN CONCLUSION

Excess of KRP4 in the developing kernels in rice causes poor filling of the grains possibly through inhibition of CDKA;2 and CDKB;1 activity mediated by its interaction with CDKF;3. The potential yield of the rice varieties producing compact and heavy panicles bearing numerous spikelets is compromised because a high percentage of spikelets remain poorly filled, reportedly because of a high expression of KRPs that causes suppression of endosperm cell proliferation. To test the stated negative relationship between KRP expression and grain filling, Orysa;KRP4 was overexpressed under the control of seed-specific glutelin promoter in IR-64 rice variety that shows good grain filling. The transgenic lines showed more than 15-fold increase in expression of KRP4 in the spikelets concomitant with nearly 50% reduction in grain filling compared with the wild type without producing any significant changes on the other yield-related parameters like panicle length and the spikelets numbers that were respectively 30.23 ± 0.89 cm and 229.25 ± 33.72 per panicle in the wild type, suggesting a highly organ-targeted effect of the genetic transformation. Yeast two-hybrid test revealed CDKF;3 as the interacting partner of KRP4, and CDKF;3 was found to interact with CDKA;2, CDKB;1 and CDKD;1. Significant decrease in grain filling in the transgenic lines compared with the wild type due to overexpression of KRP4 could be because of suppression of the activity of CDKB;1 and CDKA;2 by inhibition of their phosphorylation directly by CDKF;3, or mediated through inhibition of phosphorylation of CDKD;1 by CDKF;3. The study thus indicated that suppression of expression of KRP(s) by genetic manipulation of their promoters could be an important way of improving the yield of the rice varieties bearing compact and heavy panicles.

Anatomical insights into the vascular layout of the barley rachis: implications for transport and spikelet connection

BACKGROUND AND AIMS

Vascular patterning is intimately related to plant form and function. Here, using barley (Hordeum vulgare) as a model, we studied the vascular anatomy of the spike-type inflorescence. The main aim of the present work was to clarify the relationship between rachis (spike axis) vasculature and spike size, to define vascular dynamics and to discuss the implications for transport capacity and its interaction with the spikelets.

METHODS

We used serial transverse internode sections to determine the internode area, vascular area and number of veins along the rachis of several barley lines.

KEY RESULTS

Internode area and total vascular area show a clear positive correlation with spike size, whereas the number of veins is only weakly correlated. The lateral periphery of the rachis contains large mature veins of constant size, whereas the central part is occupied by small immature veins. Spikelet-derived veins entering the rachis often merge with the immature rachis veins but never merge with the mature veins. An increase in floret fertility through the conversion of a two-rowed barley into an isogenic six-rowed line, in addition to a decrease in floret fertility owing to enhanced pre-anthesis tip degeneration caused by the mutation tip sterile 2.b (tst2.b), significantly affected vein size but had limited to no effects on the number of veins or internode area.

CONCLUSIONS

The rachis vasculature is the result of a two-step process involving an initial layout followed by size adjustment according to floret fertility/spike size. The restriction of large mature vessels to the periphery and that of small immature vessels to the centre of the rachis suggests that long-distance transport and local supply to spikelets are spatially separated processes. The identification of spikelet-derived veins entering the rachis without fusing with its vasculature indicates that a vascular continuity between rachis and spikelets might be non-essential.

Purine permease (PUP) family gene PUP11 positively regulates the rice seed setting rate by influencing seed development

KEY MESSAGE

Purine permease PUP11 is essential for rice seed development, regulates the seed setting rate, and influences the cytokinin content, sugar transport, and starch biosynthesis during grain development. The distribution of cytokinins in plant tissues determines plant growth and development and is regulated by several cytokinin transporters, including purine permease (PUP). Thirteen PUP genes have been identified within the rice genome; however, the functions of most of these genes remain poorly understood. We found that pup11 mutants showed extremely low seed setting rates and a unique filled seed distribution. Moreover, seed formation arrest in these mutants was associated with the disappearance of accumulated starch 10 days after flowering. PUP11 has two major transcripts with different expression patterns and subcellular locations, and further studies revealed that they have redundant positive roles in regulating the seed setting rate. We also found that type-A Response Regulator (RR) genes were upregulated in the developing grains of the pup11 mutant compared with those in the wild type. The results also showed that PUP11 altered the expression of several sucrose transporters and significantly upregulated certain starch biosynthesis genes. In summary, our results indicate that PUP11 influences the rice seed setting rate by regulating sucrose transport and starch accumulation during grain filling. This research provides new insights into the relationship between cytokinins and seed development, which may help improve cereal yield.

The Inferior Grain Filling Initiation Promotes the Source Strength of Rice Leaves

Poor grain-filling initiation in inferior spikelets severely impedes rice yield improvement, while photo-assimilates from source leaves can greatly stimulate the initiation of inferior grain-filling (sink). To investigate the underlying mechanism of source-sink interaction, a two-year field experiment was conducted in 2019 and 2020 using two large-panicle rice cultivars (CJ03 and W1844). The treatments included intact panicles and partial spikelet removal. These two cultivars showed no significant difference in the number of spikelets per panicle. However, after removing spikelet, W1844 showed higher promotion on 1000-grain weight and seed-setting rate than CJ03, particularly for inferior spikelets. The reason was that the better sink activity of W1844 led to a more effective initiation of inferior grain-filling compared to CJ03. The inferior grain weight of CJ03 and W1844 did not show a significant increase until 8 days poster anthesis (DPA), which follows a similar pattern to the accumulation of photo-assimilates in leaves. After removing spikelets, the source leaves of W1844 exhibited lower photosynthetic inhibition compared to CJ03, as well as stronger metabolism and transport of photo-assimilates. Although T6P levels remained constant in both cultivars under same conditions, the source leaves of W1844 showed notable downregulation of SnRK1 activity and upregulation of phytohormones (such as abscisic acid, cytokinins, and auxin) after removing spikelets. Hence, the high sink strength of inferior spikelets plays a role in triggering the enhancement of source strength in rice leaves, thereby fulfilling grain-filling initiation demands.

Morphological and Anatomical Analysis of the Internodes of a New Dwarf Variant of Moso Bamboo, Phyllostachys edulis f. exaurita

The lack of mutants due to the long periods between flowering of bamboo plants is one of the limiting factors inhibiting research progress in the culm development of bamboo plants. In this study, a stable new dwarf variant of Phyllostachys edulis (Moso bamboo), Phyllostachys edulis f. exaurita T. G. Chen, was discovered and was characterized morphologically, anatomically, and physiologically. The height, diameter at breast height, number of internodes, length and wall thickness of internodes, length, width and number of parenchyma cells of internodes, and morphology of the wide-type (WT) and dwarf variant vascular bundles were compared. The height of the variant was only 49% that of the WT Moso bamboo. It was concluded that the decrease in internode number and length was the cause of dwarfism in P. edulis f. exaurita. The decreased internode length was the result of a decrease in cell number and cell length in the internode. In addition, the laws of change of internode length, internode thickness, cell length, and cell number differed between the WT Moso bamboo and the variant. Furthermore, lower IAA and zeatin concentrations were detected in the buds of the variant. These results suggest that P. edulis f. exaurita is a variant with inhibited primary thickening growth, which is valuable for interpretating the molecular mechanisms underlying the primary thickening growth of bamboo that are still largely unknown.

Understanding the regulation of cereal grain filling: The way forward

During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.

Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

Brassinosteroids (BRs) regulate of maize (Zea mays L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging, likely by protecting the plant against stem rot and sheath rot. BRs had no significant effect on plant height during late growth, but it increased leaf angle and photosynthetic efficiency, as well as yield and quality traits. Our findings increase our understanding of the regulatory effects of BR on maize root growth and development and the mechanism by which BR improves disease resistance, which could further the potential for using BR to improve maize yield.

Transcriptomic and physiological analyses unravel the effect and mechanism of halosulfuron-methyl on the symbiosis between rhizobium and soybean

Halosulfuron-methyl (HSM) is a new and highly effective sulfonylurea herbicide widely used in weed control, but its residue in the environment poses a potential risk to soybean. Soybean-rhizobium symbiotic nitrogen fixation is crucial for sustainable agricultural development and ecological environment health. However, the impact of HSM on the symbiosis between soybean and rhizobium is unclear. In this study, the effects of HSM on the soybean-rhizobium symbiotic process and nitrogen fixation were investigated by means of transcriptomic and physiological analyses. Treatment with a concentration of HSM less than 0.5 mg L^-1 had no effect on rhizobium growth, but significantly reduced nodules number, the biomass of soybean nodules, and nitrogenase activity in root nodules (P < 0.05). Transcriptomic analysis showed that differentially expressed genes (DEGs) involved in NH₄⁺ assimilation were significantly downregulated (P < 0.05). In addition, the activities of NH₄⁺ assimilation enzymes were markedly reduced. This result was further confirmed by the accumulation of NH₄⁺ in root nodules, indicating that the inhibition of nitrogen fixation by HSM may be caused by excessive NH₄⁺ accumulation in root nodules. Furthermore, DEGs involved in flavonoid synthesis, phytohormone biosynthesis, and phytohormone signaling transduction were significantly downregulated (P < 0.05), which was consistent with the decrease in flavonoid and phytohormone contents determined in this study. These results suggested that HSM may inhibit soybean nodulation by inhibiting flavonoid synthesis in soybean roots, disrupting the balance of plant endogenous hormones in roots during symbiosis, and blocking the transmission of hormone signals during the symbiosis. Our findings provide new insights into the effects of HSM on the legume-rhizobium nodule symbiotic process.

Two plant growth-promoting bacterial Bacillus strains possess different mechanisms in affecting cadmium uptake and detoxification of Solanum nigrum L

Microorganisms affect cadmium (Cd) extraction by hyperaccumulators to varying degrees, but the potential mechanism has not been completely studied. Here, two plant growth-promoting bacteria (PGPB, Bacillus paranthracis NT1 and Bacillus megaterium NCT-2) were assessed for their influence on Cd uptake by Solanum nigrum L. and their influence mechanisms. The results showed that both two strains could regulate phytohormones secretion, alleviate oxidative stress and promote S. nigrum growth when exposed to Cd (dry weight was significantly increased by 21.51% (strain NCT-2) and 21.23% (strain NT1) compared with the control, respectively). Additionally, strain NCT-2 significantly elevated the translocation factor (TF) and bioconcentration factor (BCF), and thus significantly facilitated total Cd uptake by 41.80% of S. nigrum, whereas strain NT1 significantly reduced the BCF and TF, resulting in insignificant effect on total Cd uptake of S. nigrum compared with the control. Results of qPCR illustrated that the two strains influenced the detoxification of Cd in S. nigrum by affecting the expression of antioxidant enzyme genes and gene PDR2. Moreover, the differential expression of heavy metal transport genes IRT1 and HMA may lead to the difference of Cd accumulation in S. nigrum. Principal component analysis and Pearson correlation coefficient analysis further verified the positive roles of salicylic acid and indole-3-acetic acid on Cd detoxification of S. nigrum, and the positive correlation relationship between transportation of Cd from underground to shoot, plant biomass and Cd uptake. Altogether, our results demonstrated that these two PGPB have great potential in helping plants detoxify Cd and could provide insights into the mechanism of PGPB-assisted phytoremediation of Cd-contaminated soil.

Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors

Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited ∼28 mg g-1 dry weight (DW) lignin and ∼44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.

Response of Rice with Overlapping Growth Stages to Water Stress by Assimilates Accumulation and Transport and Starch Synthesis of Superior and Inferior Grains

Drought stress at jointing–booting directly affects plant growth and productivity in rice. Limited by natural factors, the jointing and booting stages of short-growth-period rice varieties are highly overlapped in high-latitude areas, which are more sensitive to water deficit. However, little is known about the dry matter translocation in rice and the strategies of starch synthesis and filling of superior and inferior grains under different drought stress was unclear. In this study, the rice plants were subjected to three degrees of drought stress (−10 kPa, −25 kPa, −40 kPa) for 15 days during the jointing–booting stage; we investigated dry matter accumulation and translocation, grain filling and enzyme activities to starch synthesis of superior and inferior grains in rice with overlapping growth stages from 2016 to 2017. The results showed that drought stress significantly reduced dry matter accumulation in the stems and leaves. Mild and moderate drought increased dry matter translocation efficiency. However, severe drought stress largely limited the dry matter accumulation and translocation. A large amount of dry matter remains in vegetative organs under severe drought stress. The high content in NSC in stem and sheath plays a key role in resisting drought stress. The drought stress at jointing–booting directly caused a change in the grain filling strategy. Under moderate and severe drought, the grain-filling active period of the superior grains was shortened to complete the necessary reproductive growth. The grain-filling active period of the inferior grains was significantly prolonged to avoid a decrease in grain yield. The significant decrease in the grain-filling rate of the superior and inferior grains caused a reduction in the thousand-grain weight. In particular, the influence of the grain-filling rate of inferior grains on the thousand-grain weight was more significant. Drought stress changed the starch synthesis strategies of the superior and inferior grains. Soluble starch synthase and starch branching enzyme activities of inferior grains increased significantly under drought stress. GBSS activity was not sensitive to drought stress. Therefore, amylose content was decreased and amylopectin synthesis was enhanced under drought stress, especially in inferior grains.

Genes determining panicle morphology and grain quality in rice (Oryza sativa)

The world's increase in rice (Oryza sativa L.) production is not keeping up with the increase in its population. To boost the introduction of new high-yielding cultivars, knowledge is being gained on the genes and quantitative trait loci (QTLs) determining the panicle phenotype. The important are those determining yield of the crop, such as grain numbers per panicle and size and weight of the grains. Biochemical and molecular functions of many of them are understood in some details. Among these, OsCKX2 and OsSPL14 have been shown to increase panicle branching and grain numbers when overexpressed. Furthermore, miRNAs appear to play an important role in determining the panicle morphology by regulating the expressions of the genes like OsSPL14 and GRF4 involved in panicle branching and grain numbers and length. Mutations also greatly influence the grain shape and size. However, the information gained so far on the genetic regulation of grain filling and panicle morphology has not been successfully put into commercial application. Furthermore, the identification of the gene(s)/QTLs regulating panicle compactness is still lacking, which may enable the researchers to convert a compact-panicle cultivar into a lax/open one, and thereby increasing the chances of enhancing the yield of a desired compact-panicle cultivar obtained by the breeding effort.

Effect of Panicle Morphology on Grain Filling and Rice Yield: Genetic Control and Molecular Regulation

The demand for rice is likely to increase approximately 1.5 times by the year 2050. In contrast, the rice production is stagnant since the past decade as the ongoing rice breeding program is unable to increase the production further, primarily because of the problem in grain filling. Investigations have revealed several reasons for poor filling of the grains in the inferior spikelets of the compact panicle, which are otherwise genetically competent to develop into well-filled grains. Among these, the important reasons are 1) poor activities of the starch biosynthesizing enzymes, 2) high ethylene production leading to inhibition in expressions of the starch biosynthesizing enzymes, 3) insufficient division of the endosperm cells and endoreduplication of their nuclei, 4) low accumulation of cytokinins and indole-3-acetic acid (IAA) that promote grain filling, and 5) altered expressions of the miRNAs unfavorable for grain filling. At the genetic level, several genes/QTLs linked to the yield traits have been identified, but the information so far has not been put into perspective toward increasing the rice production. Keeping in view the genetic competency of the inferior spikelets to develop into well-filled grains and based on the findings from the recent research studies, improving grain filling in these spikelets seems plausible through the following biotechnological interventions: 1) spikelet-specific knockdown of the genes involved in ethylene synthesis and overexpression of β-CAS (β-cyanoalanine) for enhanced scavenging of CN⁻ formed as a byproduct of ethylene biosynthesis; 2) designing molecular means for increased accumulation of cytokinins, abscisic acid (ABA), and IAA in the caryopses; 3) manipulation of expression of the transcription factors like MYC and OsbZIP58 to drive the expression of the starch biosynthesizing enzymes; 4) spikelet-specific overexpression of the cyclins like CycB;1 and CycH;1 for promoting endosperm cell division; and 5) the targeted increase in accumulation of ABA in the straw during the grain filling stage for increased carbon resource remobilization to the grains. Identification of genes determining panicle compactness could also lead to an increase in rice yield through conversion of a compact-panicle into a lax/open one. These efforts have the ability to increase rice production by as much as 30%, which could be more than the set production target by the year 2050.

Biochemical and molecular processes contributing to grain filling and yield in rice

The increase in much required rice production through breeding programmes is on decline. The primary reason being poor filling of grains in the basal spikelets of the heavy and compact panicle rice developed. These spikelets are genetically competent to develop into well filled grains, but fail to do so because the carbohydrate assimilates available to them remain unutilized, reportedly due to poor activities of the starch biosynthesizing enzymes, high production of ethylene leading to enhanced synthesis of the downstream signaling component RSR1 protein that inhibits GBSS1 activity, poor endosperm cell division and endoreduplication of the endosperm nuclei, altered expression of the transcription factors influencing grain filling, enhanced expression and phosphorylation of 14-3-3 proteins, poor expression of the seed storage proteins, reduced synthesis of the hormones like cytokinins and IAA that promote grain filling, and altered expression of miRNAs preventing their normal role in grain filling. Since the basal spikelets are genetically competent to develop into well filled mature grains, biotechnological interventions in terms of spikelet-specific overexpression of the genes encoding enzymes involved in grain filling and/or knockdown/overexpression of the genes influencing the activities of the starch biosynthesizing enzymes, various cell cycle events and hormone biosynthesis could increase rice production by as much as 30%, much more than the set production target of 800 mmt. Application of these biotechnological interventions in the heavy and compact panicle cultivars producing grains of desired quality would also maintain the quality of the grains having demand in market besides increasing the rice production per se.

Sink Strength Promoting Remobilization of Non-Structural Carbohydrates by Activating Sugar Signaling in Rice Stem during Grain Filling

The remobilization of non-structural carbohydrates (NSCs) in the stem is essential for rice grain filling so as to improve grain yield. We conducted a two-year field experiment to deeply investigate their relationship. Two large-panicle rice varieties with similar spikelet size, CJ03 and W1844, were used to conduct two treatments (removing-spikelet group and control group). Compared to CJ03, W1844 had higher 1000-grain weight, especially for the grain growth of inferior spikelets (IS) after removing the spikelet. These results were mainly ascribed to the stronger sink strength of W1844 than that of CJ03 contrasting in the same group. The remobilization efficiency of NSC in the stem decreased significantly after removing the spikelet for both CJ03 and W1844, and the level of sugar signaling in the T6P-SnRK1 pathway was also significantly changed. However, W1844 outperformed CJ03 in terms of the efficiency of carbon reserve remobilization under the same treatments. More precisely, there was a significant difference during the early grain-filling stage in terms of the conversion of sucrose and starch. Interestingly, the sugar signaling of the T6P and SnRK1 pathways also represented an obvious change. Hence, sugar signaling may be promoted by sink strength to remobilize the NSCs of the rice stem during grain filling to further advance crop yield.

Relationship Between the Vascular Bundle Structure of Panicle Branches and the Filling of Inferior Spikelets in Large-Panicle Japonica Rice

The vascular bundles of rice panicles serve to connect the source and the sink, as well as serving as a channel for the transportation of materials. In this study, two homozygous japonica rice strains were used as materials. The vascular bundle structures of the branches in different positions within a rice panicle were observed, and their cross-sectional areas were calculated. In addition, the ultrastructure of the central large vascular bundle (LVB) phloem in the rachillae of superior spikelets (SS) and inferior spikelets (IS) was observed during the grain filling period. Moreover, the soluble sugar and protein contents of the SS and IS rachillae were also measured to study whether the differences in the structure of vascular bundles of the branches were related to the plumpness of grain at different positions. The results showed that vascular bundle cross-sectional areas of the basal primary branches were greater than those in the upper primary branches. Moreover, there was little difference in the areas of vascular bundles between the basal secondary branches and upper secondary branches. However, the vascular bundle areas of the IS rachillae were lower than those in the SS rachillae. Therefore, we believe that the poor vascular tissue channel of the IS rachillae could be the limiting factor in IS plumpness. The results also showed that a similar time course in the degradation pattern of some organelles of the sieve elements and companion cells in central LVB was observed in the SS rachillae and IS rachillae during the grain filling period. Compared with the IS rachillae, more abundant mitochondria and plasmodesmata were found in the companion cells of SS rachillae at the beginning of the filling stage, while no significant differences between SS and IS rachillae were identified at the middle and late filling stages, which implies that the SS rachillae were relatively more effective at transportation compared with the IS rachillae at the initial filling stage. Therefore, the undeveloped vascular bundles of the IS rachillae and their poor physiology and lack of ability to transport at the initial filling stages could be the limiting factor in IS plumpness.

Metabolic factors restricting sink strength in superior and inferior spikelets in high-yielding rice cultivars

Many high-yielding rice cultivars with large sink size (total number of spikelet per unit area × mean grain weight) have been developed, but some japonica cultivars developed in Japan often fail to attain the expected high yield due to low sink strength of spikelets. Although there is natural variation in sink strength of spikelets among high-yielding cultivars, metabolic factors involved in the natural variation and relationships of sink strength in spikelets with final percentage of filled spikelets are not fully understood. In the present study, we examined cultivar differences in sink strength for superior and inferior spikelets (i.e. earlier fertilizing spikelets with faster growth and later fertilizing ones with slower growth, respectively) in a panicle, using each spikelet at 10 d after the onset of development (10 DAD) when starch accumulation in endosperm was actively proceeding. Nine high-yielding cultivars were used: five japonica-dominant and four indica-dominant cultivars. Cultivar differences were observed in starch contents at 10 DAD in each spikelet type, and indica cultivars had higher starch contents than japonica cultivars in both superior and inferior spikelets. In addition, starch contents at 10 DAD were closely related to percentage of filled grains at maturity in both spikelet types. The activities of sucrose synthase (SUS) and uridine diphosphoglucose pyrophosphorylase (UGP), and the protein levels of phosphorylase 1 (Pho1), were higher in indica than japonica cultivars, and were positively correlated with starch contents at 10 DAD for both superior and inferior spikelets; although metabolic states, revealed from relations between intermediate metabolites and starch contents, differed among spikelet types. Consequently, it was considered that SUS and UGP at the step from sucrose cleavage to adenosine diphosphoglucose synthesis, and Pho1 at the starch biosynthesis step, were key metabolic factors involved in cultivar differences of sink strength (ability to synthesize starch).

Cerium-Promoted Ginsenosides Accumulation by Regulating Endogenous Methyl Jasmonate Biosynthesis in Hairy Roots of Panax ginseng

Among rare earth elements, cerium has the unique ability of regulating the growth of plant cells and the biosynthesis of metabolites at different stages of plant development. The signal pathways of Ce3+-mediated ginsenosides biosynthesis in ginseng hairy roots were investigated. At a low concentration, Ce3+ improved the elongation and biomass of hairy roots. The Ce3+-induced accumulation of ginsenosides showed a high correlation with the reactive oxygen species (ROS), as well as the biosynthesis of endogenous methyl jasmonate (MeJA) and ginsenoside key enzyme genes (PgSS, PgSE and PgDDS). At a Ce3+ concentration of 20 mg L-1, the total ginsenoside content was 1.7-fold, and the total ginsenosides yield was 2.7-fold that of the control. Malondialdehyde (MDA) content and the ROS production rate were significantly higher than those of the control. The activity of superoxide dismutase (SOD) was significantly activated within the Ce3+ concentration range of 10 to 30 mg L-1. The activity of catalase (CAT) and peroxidase (POD) strengthened with the increasing concentration of Ce3+ in the range of 20-40 mg L-1. The Ce3+ exposure induced transient production of superoxide anion (O2•-) and hydrogen peroxide (H2O2). Together with the increase in the intracellular MeJA level and enzyme activity for lipoxygenase (LOX), there was an increase in the gene expression level of MeJA biosynthesis including PgLOX, PgAOS and PgJMT. Our results also revealed that Ce3+ did not directly influence PgSS, PgSE and PgDDS activity. We speculated that Ce3+-induced ROS production could enhance the accumulation of ginsenosides in ginseng hairy roots via the direct stimulation of enzyme genes for MeJA biosynthesis. This study demonstrates a potential approach for understanding and improving ginsenoside biosynthesis that is regulated by Ce3+-mediated signal transduction.

Efficiency of Sucrose to Starch Metabolism Is Related to the Initiation of Inferior Grain Filling in Large Panicle Rice

The poor grain-filling initiation often causes the poor development of inferior spikelets (IS) which limits the yield potential of large panicle rice (Oryza sativa L.). However, it remains unclear why IS often has poor grain-filling initiation. In addressing this problem, this study conducted a field experiment involving two large panicle rice varieties, namely CJ03 and W1844, in way of removing the superior spikelets (SS) during flowering to force enough photosynthate transport to the IS. The results of this study showed that the grain-filling initiation of SS was much earlier than the IS in CJ03 and W1844, whereas the grain-filling initiation of IS in W1844 was evidently more promoted compared with the IS of CJ03 by removing spikelets. The poor sucrose-unloading ability, i.e., carbohydrates contents, the expression patterns of OsSUTs, and activity of CWI, were highly improved in IS of CJ03 and W1844 by removing spikelets. However, there was a significantly higher rise in the efficiency of sucrose to starch metabolism, i.e., the expression patterns of OsSUS4 and OsAGPL1 and activities of SuSase and AGPase, for IS of W1844 than that of CJ03. Removing spikelets also led to the changes in sugar signaling of T6P and SnRK1 level. These changes might be related to the regulation of sucrose to starch metabolism. The findings of this study suggested that poor sucrose-unloading ability delays the grain-filling initiation of IS. Nonetheless, the efficiency of sucrose to starch metabolism is also strongly linked with the grain-filling initiation of IS.

Salicylic acid underpins silicon in ameliorating chromium toxicity in rice by modulating antioxidant defense, ion homeostasis and cellular ultrastructure

Chromium (Cr) phytotoxicity affirmed the need of mitigation strategies to remediate polluted soils and restricts its accumulation in the food chains. Salicylic acid (SA) and silicon (Si) play pivotal roles in stimulating the plant performance and stress resilience. So far, their interactive effects against Cr-phytotoxicities are less known. Thus, we evaluated the beneficial roles of alone or/and combine applications of SA and Si in mitigating the toxic effects of Cr in the leaves and roots of rice (Oryza sativa) seedlings. Results indicated that SA (10 μM) and/or Si (5 μM) markedly retrieved the Cr (100 μM) induced toxicities by minimizing the Cr-accretion in both leaves and roots, enhancing the performance of light harvesting pigments (total chlorophylls and carotenoids), water retention and accumulation of osmolytes (water-soluble protein and total soluble sugars) and ultimately improved the growth and biomass. Additionally, SA and/or Si maintained the ionic balance by enhancing the nutrients transport, upregulated the ascorbate-glutathione (AsA-GSH) cycle enzymes, minimized the extra accumulation of reactive oxygen species (ROS) (H₂O₂ and O₂^•‒), malondialdehyde (MDA), recovered the membrane stability and damages in cellular ultrastructure in Cr-stressed rice plants. Overall findings suggested that SA underpins Si in mitigating the Cr-induced phytotoxicities on the above-reported parameters and combined applications of SA and Si were more effective than alone treatments. The uptake or cellular accumulation of Cr, osmoprotectants level and antioxidant defense system against oxidative stress can be considered as key toxicity biomarkers for the safe cultivation of rice in Cr-contaminated soils.

A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity

Carbohydrate metabolism is an important biochemical process related to developmental growth and yield-related traits. Due to global climate change and rapid population growth, increasing rice yield has become vital. To understand whole carbohydrate metabolism pathways and find related clues for enhancing yield, genes in whole carbohydrate metabolism pathways were systemically dissected using meta-transcriptome data. This study identified 866 carbohydrate genes from the MapMan toolkit and the Kyoto Encyclopedia of Genes and Genomes database split into 11 clusters of different anatomical expression profiles. Analysis of functionally characterized carbohydrate genes revealed that source activity and eating quality are the most well-known functions, and they each have a strong correlation with tissue-preferred clusters. To verify the transcriptomic dissection, three pollen-preferred cluster genes were used and found downregulated in the gori mutant. Finally, we summarized carbohydrate metabolism as a conceptual model in gene clusters associated with morphological traits. This systemic analysis not only provided new insights to improve rice yield but also proposed novel tissue-preferred carbohydrate genes for future research.

Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

Source-Sink Manipulation Affects Accumulation of Zinc and Other Nutrient Elements in Wheat Grains

To better understand the source–sink flow and its relationships with zinc (Zn) and other nutrients in wheat (Triticum aestivum L.) plants for biofortification and improving grain nutritional quality, the effects of reducing the photoassimilate source (through the flag leaf removal and spike shading) or sink (through the removal of all spikelets from one side of the spike, i.e., 50% spikelets removal) in the field of the accumulation of Zn and other nutrients in grains of two wheat cultivars (Jimai 22 and Jimai 44) were investigated at two soil Zn application levels. The kernel number per spike (KNPS), single panicle weight (SPW), thousand kernel weight (TKW), total grain weight (TGW) sampled, concentrations and yields of various nutrient elements including Zn, iron (Fe), manganese (Mn), copper (Cu), nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and magnesium (Mg), phytate phosphorus (phytate-P), phytic acid (PA) and phytohormones (ABA: abscisic acid, and the ethylene precursor ACC: 1-aminocylopropane-1-carboxylic acid), and carbon/N ratios were determined. Soil Zn application significantly increased the concentrations of grain Zn, N and K. Cultivars showing higher grain yields had lower grain protein and micronutrient nutritional quality. SPW, KNPS, TKW (with the exception of TKW in the removal of half of the spikelets), TGW, and nutrient yields in wheat grains were most severely reduced by half spikelet removal, secondly by spike shading, and slightly by flag leaf removal. Grain concentrations of Zn, N and Mg consistently showed negative correlations with SPW, KNPS and TGW, but positive correlations with TKW. There were general positive correlations among grain concentrations of Zn, Fe, Mn, Cu, N and Mg, and the bioavailability of Zn and Fe (estimated by molar ratios of PA/Zn, PA/Fe, PA × Ca/Zn, or PA × Ca/Fe). Although Zn and Fe concentrations were increased and Ca was decreased in treatments of half spikelet removal and spike shading, the treatments simultaneously increased PA and limited the increase in bioavailability of Zn and Fe. In general, different nutrient elements interact with each other and are affected to different degrees by source–sink manipulation. Elevated endogenous ABA levels and ABA/ACC ratios were associated with increased TKW and grain-filling of Zn, Mn, Ca and Mg, and inhibited K in wheat grains. However, the effects of ACC were diametrically opposite. These results provide a basis for wheat grain biofortification to alleviate human malnutrition.

Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain

The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains.

Transcriptome analysis reveals key genes regulating signaling and metabolic pathways during the growth of moso bamboo (Phyllostachys edulis) shoots

Moso bamboo (Phyllostachys edulis), a high-value bamboo used to produce food (young shoots), building, and industrial goods. To explore key candidate genes regulating signal transduction and metabolic processes during the initiation of stem elongation in moso bamboo, a transcriptome analysis of the shoots during three successive early elongation stages was performed. From cluster and differential expression analyses, 2984 differentially expressed genes (DEGs) were selected for an enrichment analysis. The DEGs were significantly enriched in the plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways. Consequently, the DEG expression patterns of these pathways were analyzed, and the plant endogenous hormone and carbon metabolite (including sucrose, total soluble sugar, and starch) contents for each growth stage, of the shoot, were determined. The cytokinin-signaling pathway was continuously active in the three successive elongation stages, in which several cytokinin-signaling genes played indispensable roles. Additionally, many key DEGs regulating sugar, starch metabolism, and energy conversion, which are actively involved in energy production and substrate synthesis during the continuous growth of the shoots, were found. In summary, our study lays a foundation for understanding the mechanisms of moso bamboo growth and provides useful gene resources for breeding through genetic engineering.

Analysis of carbon flow at the metabolite level reveals that starch synthesis from hexose is a limiting factor in a high-yielding rice cultivar

Understanding the limiting factors of grain filling is essential for the further improvement of grain yields in rice (Oryza sativa). The relatively slow grain growth of the high-yielding cultivar 'Momiroman' is not improved by increasing carbon supply, and hence low sink activity (i.e. the metabolic activity of assimilate consumption/storage in sink organs) may be a limiting factor for grain filling. However, there is no metabolic evidence to corroborate this hypothesis, partly because there is no consensus on how to define and quantify sink activity. In this study, we investigated the carbon flow at a metabolite level from photosynthesis in leaves to starch synthesis in grains of three high-yielding cultivars using the stable isotope 13C. We found that a large amount of newly fixed carbon assimilates in Momiroman was stored as hexose instead of being converted to starch. In addition, the activity of ADP-glucose pyrophosphorylase and the expression of AGPS2b, which encodes a subunit of the ADP-glucose pyrophosphorylase enzyme, were both lower in Momiroman than in the other two cultivars in grains in superior positions on panicle branches. Hence, slower starch synthesis from hexose, which is partly explained by the low expression level of AGPS2b, may be the primary metabolic reason for the lower sink activity observed in Momiroman.

Auxin-Mediated Regulation of Dorsal Vascular Cell Development May Be Responsible for Sucrose Phloem Unloading in Large Panicle Rice

Large panicle rice cultivars often fail to fulfill their high-yield potential due to the poor grain filling of inferior spikelets (IS), which appears as initially stagnant development and low final seed weight. Understanding the mechanism of the initial stagnancy is important to improve IS grain filling. In this study, superior spikelets (SS) were removed from two homozygous japonica rice varieties (W1844 and CJ03) with the same sink capacity in an attempt to force photosynthate transport to the IS. The results showed that SS removal increased the grain weight, sucrose content, starch accumulation, and endogenous IAA levels of IS during the initial grain-filling stage. SS removal also improved the patterns of vascular cells in the dorsal pericarp and the expression levels of genes involved in sucrose transport (OsSUTs and OsSWEETs) and IAA metabolism (OsYUCs and OsPINs). Exogenous IAA application advanced the initiation of grain filling by increasing the sucrose content and the gene expression levels of sucrose transporters. These results indicate that auxin may act like a signal substance and play a vital role in initial grain filling by regulating dorsal vascular cell development and sucrose phloem unloading into caryopsis.

Study of expressions of miRNAs in the spikelets based on their spatial location on panicle in rice cultivars provided insight into their influence on grain development

Development of rice cultivars bearing numerous spikelets by breeding approach to increase the yearly production of rice to approximately 800 million metric tons to feed the ever increasing population of the world accompanies poor grain filling in the inferior spikelets preventing achievement of the yield potential. As the initial stages of caryopses development are of much importance for grain filling, spatio-temporal expressions of the miRNAs were studied during these periods in the spikelets of a compact-panicle rice cultivar, Oryza sativa cv. Mahalaxmi, bearing numerous spikelets per panicle to understand the reason of poor grain filling at the level of the initial biochemical events. Differential expression of several known miRNAs between the superior and inferior spikelets suggested great difference in metabolism related to grain filling in the spikelets based on their spatial location on compact panicle. Expressions of five known and four novel miRNAs were validated by Northern. Their targets included the enzymes directly involved in starch biosynthesis like sucrose synthase, starch synthase and pullulanase, besides others. Spatio-temporal expression studies of these miRNAs in the spikelets of Mahalaxmi revealed a pattern of mostly a greater expression in the inferior spikelets compared with the superior ones concomitant with an inverse expression of the target genes, which was not observed in the lax-panicle cultivar Upahar. The study thus revealed that the grain filling in rice is greatly regulated by miRNAs, and these miRNAs or their target genes could be considered for biotechnological interventions for improving grain filling in the rice cultivars of interest.

The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (♀)/9311 (♂) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.

The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (♀)/9311 (♂) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.

NSs, the Silencing Suppressor of Tomato Spotted Wilt Orthotospovirus, Interferes With JA-Regulated Host Terpenoids Expression to Attract Frankliniella occidentalis

Tomato spotted wilt orthotospovirus (TSWV) causes serious crop losses worldwide and is transmitted by Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae). NSs protein is the silencing suppressor of TSWV and plays an important role in virus infection, cycling, and transmission process. In this research, we investigated the influences of NSs protein on the interaction of TSWV, plants, and F. occidentalis with the transgenic Arabidopsis thaliana. Compared with the wild-type Col-0 plant, F. occidentalis showed an increased number and induced feeding behavior on transgenic Arabidopsis thaliana expressing exogenous NSs. Further analysis showed that NSs reduced the expression of terpenoids synthesis-related genes and the content of monoterpene volatiles in Arabidopsis. These monoterpene volatiles played a repellent role in respect to F. occidentalis. In addition, the expression level of plant immune-related genes and the content of the plant resistance hormone jasmonic acid (JA) in transgenic Arabidopsis were reduced. The silencing suppressor of TSWV NSs alters the emission of plant volatiles and reduces the JA-regulated plant defenses, resulting in enhanced attractiveness of plants to F. occidentalis and may increase the transmission probability of TSWV.

Leaf Gas Exchange of Tomato Depends on Abscisic Acid and Jasmonic Acid in Response to Neighboring Plants under Different Soil Nitrogen Regimes

High planting density and nitrogen shortage are two important limiting factors for crop yield. Phytohormones, abscisic acid (ABA), and jasmonic acid (JA), play important roles in plant growth. A pot experiment was conducted to reveal the role of ABA and JA in regulating leaf gas exchange and growth in response to the neighborhood of plants under different nitrogen regimes. The experiment included two factors: two planting densities per pot (a single plant or four competing plants) and two N application levels per pot (1 and 15 mmol·L-1). Compared to when a single plant was grown per pot, neighboring competition decreased stomatal conductance (gs), transpiration (Tr) and net photosynthesis (Pn). Shoot ABA and JA and the shoot-to-root ratio increased in response to neighbors. Both gs and Pn were negatively related to shoot ABA and JA. In addition, N shortage stimulated the accumulation of ABA in roots, especially for competing plants, whereas root JA in competing plants did not increase in N15. Pearson's correlation coefficient (R2) of gs to ABA and gs to JA was higher in N1 than in N15. As compared to the absolute value of slope of gs to shoot ABA in N15, it increased in N1. Furthermore, the stomatal limitation and non-stomatal limitation of competing plants in N1 were much higher than in other treatments. It was concluded that the accumulations of ABA and JA in shoots play a coordinating role in regulating gs and Pn in response to neighbors; N shortage could intensify the impact of competition on limiting carbon fixation and plant growth directly.

Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo

Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.

Unraveling candidate genomic regions responsible for delayed leaf senescence in rice

Photosynthates generated after heading contributes to 60% - 80% of grain yield in rice. Delay in leaf senescence can contribute to a long grain-filling period and thereby increased yield. The objective of this study was to identify genomic region(s) responsible for delayed leaf senescence (DLS) and validate the role of underlying candidate genes in controlling target traits. 302 BC₂F₄ backcross-derived lines (BILs) developed from a cross between Swarna and Moroberekan were phenotyped for two seasons (DS2016 and WS2017) for chlorophyll content and yield parameters. KASPar-SNP assays based genotyping data with 193 SNPs of mapping population was used to identify the targeted genomic region(s). Significant positive correlation was observed between the two most important determinants of DLS traits viz., RDCF (reduced decline degree of chlorophyll content of flag leaf) and RDCS (reduced decline degree of chlorophyll content of second leaf) with plant height (PH), grain number per panicle (GPN), panicle length (PL), number of tiller (NT) and grain yield (GY). A total of 41 and 29 QTLs with phenotypic variance (PVE) ranging from 8.2 to 25.1% were detected for six DLS traits during DS2016 and WS2017, respectively. Out of these identified QTLs, 19 were considered as stable QTLs detected across seasons. 17 of the identified stable QTLs were found to be novel. In-silico analysis revealed five key genes regulating chlorophyll metabolism. Expression analysis of these genes confirmed their strong association with the senescence pattern in leaf tissue of parents as well as selected phenotypically extreme lines. The identified stable QTLs regulating DLS traits and validation of potential candidate genes provides insight into genetic basis of delayed senescence and is expected to contribute in enhancing grain yield through genomics-assisted breeding (GAB).

Genotypic variation in the grain photosynthetic contribution to grain filling in rice

Grain filling in rice, a staple cereal crop worldwide, is a critical determinant of grain yield and quality. However, there is little available information on the relationship between grain filling and grain photosynthetic capacity in rice. This study evaluated the genetic diversity among six rice cultivars for their grain filling rate (GR₀) and the relationships with the grain chlorophyll contents and grain net photosynthetic rate (P_N). Significant variations in GR₀, P_N, and the chlorophyll contents (a, b, and total) in the grains of the cultivars were observed. Approximately 90 % of the variation in GR₀ was explained by the grain P_N. General linear model regression revealed significant positive correlations between P_N/GR₀ and the chlorophyll contents (a, b, and total) in the grains. There was also a significant positive correlation between P_N and GR₀. These positive correlations suggest a direct positive relationship between the grain filling rate and grain chlorophyll contents, which is indicative of the high photosynthetic capacity of the grains during the early grain filling period. These results suggest that the grain chlorophyll contents could be used as a molecular marker in marker-assisted breeding programs for rice cultivars with high grain net photosynthetic capacity during the early period of grain filling to improve grain yield.

Pyridoxal 5'-phosphate enhances the growth and morpho-physiological characteristics of rice cultivars by mitigating the ethylene accumulation under salinity stress

Salinity-induced ethylene accumulation caused by high production of 1-aminocyclopropane-1-carboxylic acid (ACC) hinders rice plant growth and development. Nevertheless, ACC deaminase may alleviate salt stress and high ethylene production in rice cultivars under salinity stress. Pyridoxal 5'-phosphate (PLP), an ACC deaminase co-factor, could be a useful ACC inhibitor in plants; however, it has not been studied before. In the present study, the effects of PLP on the growth and morphophysiological characteristics of rice cultivars (Jinyuan 85 (JY85) and Nipponbare (NPBA) were investigated under salinity stress (control (CK), low salinity (LS), and high salinity (HS) in hydroponic conditions. The experiment was laid out in a completely randomized design (CRD) under factorial arrangement of treatments. The results showed that, compared with no PLP, exogenous application of PLP significantly inhibited ACC and ethylene production in the roots, leaves and panicles of both cultivars under salinity, and PLP was more effective at improving the physiological characteristics of both cultivars under salinity stress. Further, root morphophysiological traits and pollen viability were triggered in the PLP treatment compared to the no-PLP treatment under various salinity levels. ACC production inhibited by PLP was useful for improving the 1000-grain weight, grain yield per plant, and total plant biomass under the CK, LS and HS treatments in both rice cultivars. These results revealed that PLP, as an ACC deaminase cofactor, is a key tool for mitigating ethylene-induced effects under salinity stress and for enhancing the agronomic and morphophysiological traits of rice under saline conditions.

The WUSCHEL-related homeobox transcription factor OsWOX4 controls the primary root elongation by activating OsAUX1 in rice

Primary root is the basic component of root system and plays a key role in early seedling growth and survival in rice. However, the molecular mechanism of primary root elongation still needs to be well understood. Here, we showed that OsWOX4, a WUSCHEL-related homeobox (WOX) transcription factor, was involved in the primary root elongation in rice. Silencing of OsWOX4 by RNA interference (RNAi) greatly increased the primary root length, whereas its overexpression reduced primary root elongation significantly. Moreover, the size of meristem zone and epidermal cell length of mature zone in RNAi root tips were drastically enhanced, while they were reduced markedly in overexpression lines, in comparison with that of wild type. Further analysis showed that the accumulation of free IAA was slightly increased in RNAi roots, but drastically reduced in plants overexpressing OsWOX4. The expression of genes responsible for auxin biosynthesis and transport was also changed in OsWOX4 transgenic lines. Transient transcriptional activation and electrophoretic mobility shift assays showed that OsWOX4 directly regulated the transcription of OsAUX1 through binding to its promoter region. Collectively, our results indicated that OsWOX4 played a crucial role in the primary root elongation by regulating auxin transport, suggesting its importance in rice root system architecture.

CpARF2 and CpEIL1 interact to mediate auxin-ethylene interaction and regulate fruit ripening in papaya

Papaya (Carica papaya L.) is a commercially important fruit crop. Various phytohormones, particularly ethylene and auxin, control papaya fruit ripening. However, little is known about the interaction between auxin and ethylene signaling during the fruit ripening process. In the present study, we determined that the interaction between the CpARF2 and CpEIL1 mediates the interaction between auxin and ethylene signaling to regulate fruit ripening in papaya. We identified the ethylene-induced auxin response factor CpARF2 and demonstrated that it is essential for fruit ripening in papaya. CpARF2 interacts with an important ethylene signal transcription factor CpEIL1, thus increasing the CpEIL1-mediated transcription of the fruit ripening-associated genes CpACS1, CpACO1, CpXTH12 and CpPE51. Moreover, CpEIL1 is ubiquitinated by CpEBF1 and is degraded through the 26S proteasome pathway. However, CpARF2 weakens the CpEBF1-CpEIL1 interaction and interferes with CpEBF1-mediated degradation of CpEIL1, promoting fruit ripening. Therefore, CpARF2 functions as an integrator in the auxin-ethylene interaction and regulates fruit ripening by stabilizing CpEIL1 protein and promoting the transcriptional activity of CpEIL1. To our knowledge, we have revealed a novel module of CpARF2/CpEIL1/CpEBF1 that fine-tune fruit ripening in papaya. Manipulating this mechanism could help growers tightly control papaya fruit ripening and prolong shelf life.

Pleiotropic Effect of GNP1 Underlying Grain Number per Panicle on Sink, Source and Flow in Rice

Rice yield potential is largely determined by the balance among source capacity, sink strength, and flow fluency. Our previous study indicated that the gene GNP1 encoding gibberellin biosynthesis gene GA20ox1 affects grain number per panicle (GNP) in rice, thus resulting in increase of grain yield. To clarify GNP1 effect on sink, source and flow in regulating rice grain yield, we compared Lemont, a japonica (geng) cultivar, with its near-isogenic line (NIL-GNP1 ^TQ) in Lemont background with introgression of the allele at GNP1 from Teqing, a high-yielding indica (xian) cultivar. NIL-GNP1 ^TQ exhibited averagely 32.8% more GNP than Lemont with the compensation by reduced seed setting rate, panicle number and single-grain weight. However, NIL-GNP1 ^TQ still produced averagely 7.2% higher grain yield than Lemont in two years, mainly attributed to significantly more filled grain number per panicle, and greater vascular system contributing to photoassimilates transport to spikelets. The significantly decreased grain weight of superior spikelets (SS) in NIL-GNP1 ^TQ was ascribed to a significant decrease of grain size while the significantly decreased grain weight of inferior spikelets (IS) ascribed to both grain size and poor grain-filling as compared with Lemont. The low activities of key enzymes of carbon metabolism might account for the poor grain-filling in IS, which resulted in more unfilled grains or small grain bulk density in NIL-GNP1 ^TQ. In addition, low seed setting rate and grain weight of IS in NIL-GNP1 ^TQ might be partially resulted from significantly lower carbohydrate accumulation in culms and leaf sheath before heading compared with Lemont. Our results indicated that significantly increased GNP from introgression of GNP1 ^TQ into Lemont did not highly significantly improve grain yield of NIL-GNP1 ^TQ as expected, due primarily to significant low sink activities in IS and possible insufficient source supply which didn't fully meet the increased sink capacity. The results provided useful information for improving rice yield potential through reasonably introgressing or pyramiding the favorable alleles underlying source-related or panicle number traits by marker-assisted selection.

Major Latex Protein MdMLP423 Negatively Regulates Defense against Fungal Infections in Apple

Major latex proteins (MLPs) play critical roles in plants defense and stress responses. However, the roles of MLPs from apple (Malus × domestica) have not been clearly identified. In this study, we focused on the biological role of MdMLP423, which had been previously characterized as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis indicated that MdMLP423 is a protein with a ‘Gly-rich loop’ (GXGGXG) domain belonging to the Bet v_1 subfamily. Gene expression profiles showed that MdMLP423 is mainly expressed in flowers. In addition, the expression of MdMLP423 was significantly inhibited by Botryosphaeria berengeriana f. sp. piricola (BB) and Alternaria alternata apple pathotype (AAAP) infections. Apple calli overexpressing MdMLP423 had lower expression of resistance-related genes, and were more sensitive to infection with BB and AAAP compared with non-transgenic calli. RNA-seq analysis of MdMLP423-overexpressing calli and non-transgenic calli indicated that MdMLP423 regulated the expression of a number of differentially expressed genes (DEGs) and transcription factors, including genes involved in phytohormone signaling pathways, cell wall reinforcement, and genes encoding the defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein, and ABI3. Taken together, our results demonstrate that MdMLP423 negatively regulates apple resistance to BB and AAAP infections by inhibiting the expression of defense- and stress-related genes and transcription factors.

Characterization and Grouping of All Primary Branches at Various Positions on a Rice Panicle Based on Grain Growth Dynamics

Grain filling can directly influence rice yield. However, there is limited information on the growth relationship among grains at different positions on the entire panicle during grain filling. In this study, field experiments were conducted in 2014–2015 to compare the growth dynamics of grains at various positions for two rice cultivars (Nongle 1 and Guifeng 2). The results showed that a high similarity and a slow–fast–slow trend of dry-matter accumulation occurred in all primary branches. However, the maximum grain growth rates of the top primary branches were 86% and 44% higher than basal primary branches of Nongle 1 and Guifeng 2, respectively. Similarly, the maximum final grain weights were 32% and 18% greater in the top primary branches than in the basal primary branches of Nongle 1 and Guifeng 2, respectively. In contrast, the active grain filling duration was 1.5 and 1.3 times longer in the basal primary branches than the top primary branches of Nongle 1 and Guifeng 2, respectively. The time to reach the maximum rate of grain growth of the basal primary branches for Nongle 1 and Guifeng 2 was 2.2 and 2.5 times longer than those of the top primary branches, respectively. Based on cluster analysis of growth characteristics of all primary branches, Group I (superior primary-branches) was considered to be the fastest for grain filling and greatest for dry matter weight, followed by Group II (medium primary-branches). The poorest growth occurred in Group III (inferior primary-branches). Therefore, the yield of poor-filling grains at the basal panicle could be achieved primarily by improving the growth of Group III.

Proteome and transcriptome profile analysis reveals regulatory and stress-responsive networks in the russet fruit skin of sand pear

The epidermal tissues of the cuticular membrane (CM) and periderm membrane (PM) confer first-line protection from environmental stresses in terrestrial plants. Although PM protection is essentially ubiquitous in plants, the protective mechanism, the function of many transcription factors and enzymes, and the genetic control of metabolic signaling pathways are poorly understood. Different microphenotypes and cellular components in russet (PM-covered) and green (CM-covered) fruit skins of pear were revealed by scanning and transmission electron microscopy. The two types of fruit skins showed distinct phytohormone accumulation, and different transcriptomic and proteomic profiles. The enriched pathways were detected by differentially expressed genes and proteins from the two omics analyses. A detailed analysis of the suberin biosynthesis pathways identified the regulatory signaling network, highlighting the general mechanisms required for periderm formation in russet fruit skin. The regulation of aquaporins at the protein level should play an important role in the specialized functions of russet fruit skin and PM-covered plant tissues.

OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa)

BACKGROUND

FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood.

RESULTS

As a homologue of AtFPF1, FPF1-like protein 4 of rice (OsFPFL4) is expressed in various tissues of plants. The functions of OsFPFL4 in rice were investigated by the reverse genetics approaches. Plants overexpressing OsFPFL4 have shorter primary root, more lateral roots and adventitious roots than wild type; however, RNA interference (RNAi) of OsFPFL4 significantly inhibits the growth of root system, and also delays the flowering time in rice. Interestingly, increased or repressed expression of OsFPFL4 leads to shrunken anthers and abnormal pollen grains. It is well recognized that auxin plays important roles in plant root and flower development, and the root elongation is also regulated by reactive oxygen species (ROS) homeostasis. Here, our results show that rice plants overexpressing OsFPFL4 accumulate more auxin in the shoot and root, whereas RNAi lines have less auxin than wild type. As expected, the transcript levels of genes responsible for auxin biosynthesis and polar transport are altered in these OsFPFL4 transgenic plants. As to ROS, slightly higher ROS levels were detected in overexpression root and inflorescence than the counterparts of wild type; however, the ROS levels were significantly increased in the RNAi lines, due to increased expression of ROS-producers and reduced expression of ROS-scavengers.

CONCLUSION

Our results reveal that OsFPFL4 is involved in modulating the root and flower development by affecting auxin and ROS homeostasis in rice plants. OsFPFL4 controls auxin accumulation via affecting auxin biosynthesis and transport, and also modulates ROS homeostasis by balancing ROS producing and scavenging. Thus, auxin-mediated ROS production might play a role in regulating redox status, which controls plant root and flower development.

Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding

In the recent time, Submergence1 (Sub1)QTL, responsible for imparting tolerance to flash flooding, has been introduced in many rice cultivars, but resilience of the QTL to stagnant flooding (SF) is not known. The response of Sub1-introgression has been tested on physiology, molecular biology and yield of two popular rice cultivars (Swarna and Savitri) by comparison of the parental and Sub1-introgression lines (SwarnaSub1 and SavitriSub1) under SF. Compared to control condition SF reduced grain yield and tiller number and increased plant height and Sub1- introgression mostly matched these effects. SF increased ethylene production by over-expression of ACC-synthase and ACC-oxidase enzyme genes of panicle before anthesis in the parental lines. Expression of the genes changed with Sub1-introgression, where some enzyme isoform genes over-expressed after anthesis under SF. Activities of endosperm starch synthesizing enzymes SUS and AGPase declined concomitantly with rise ethylene production in the Sub1-introgressed lines resulting in low starch synthesis and accumulation of soluble carbohydrates in the developing spikelets. In conclusion, Sub1-introgression into the cultivars increased susceptibility to SF. Subjected to SF, the QTL promoted genesis of ethylene in the panicle at anthesis to the detriment of grain yield, while compromising with morphological features like tiller production and stem elongation.

Favorable Alleles of GRAIN-FILLING RATE1 Increase the Grain-Filling Rate and Yield of Rice

Hybrid rice (Oryza sativa) has been cultivated commercially for 42 years in China. However, poor grain filling still limits the development of hybrid japonica rice. We report here the map-based cloning and characterization of the GRAIN-FILLING RATE1 (GFR1) gene present at a major-effect quantitative trait locus. We elucidated and confirmed the function of GFR1 via genetic complementation experiments and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing in combination with genetic and molecular biological analyses. In addition, we conducted haplotype association analysis to mine the elite alleles of GFR1 among 117 rice accessions. We observed that GFR1 was constitutively expressed and encoded a membrane-localized protein. The allele of the rice accession Ludao (GFR1 Ludao) improved the grain-filling rate of rice by increasing Rubisco initial activity in the Calvin cycle. Moreover, the increased expression of the cell wall invertase gene OsCIN1 in the near isogenic line NIL-GFR1 Ludao promoted the unloading of Suc during the rice grain-filling stage. A yeast two-hybrid assay indicated that the Rubisco small subunit interacts with GFR1, possibly in the regulation of the rice grain-filling rate. Evaluation of the grain-filling rate and grain yield of F1 plants harboring GFR1 Ludao and the alleles of 20 hybrids widely cultivated commercially confirmed that favorable alleles of GFR1 can be used to further improve the grain-filling rate of hybrid japonica rice.

The hypersensitive induced reaction 3 (HIR3) gene contributes to plant basal resistance via an EDS1 and salicylic acid-dependent pathway

The hypersensitive-induced reaction (HIR) gene family is associated with the hypersensitive response (HR) that is a part of the plant defense system against bacterial and fungal pathogens. The involvement of HIR genes in response to viral pathogens has not yet been studied. We now report that the HIR3 genes of Nicotiana benthamiana and Oryza sativa (rice) were upregulated following rice stripe virus (RSV) infection. Silencing of HIR3s in N. benthamiana resulted in an increased accumulation of RSV RNAs, whereas overexpression of HIR3s in N. benthamiana or rice reduced the expression of RSV RNAs and decreased symptom severity, while also conferring resistance to Turnip mosaic virus, Potato virus X, and the bacterial pathogens Pseudomonas syringae and Xanthomonas oryzae. Silencing of HIR3 genes in N. benthamiana reduced the content of salicylic acid (SA) and was accompanied by the downregulated expression of genes in the SA pathway. Transient expression of the two HIR3 gene homologs from N. benthamiana or the rice HIR3 gene in N. benthamiana leaves caused cell death and an accumulation of SA, but did not do so in EDS1-silenced plants or in plants expressing NahG. The results indicate that HIR3 contributes to plant basal resistance via an EDS1- and SA-dependent pathway.

BR deficiency causes increased sensitivity to drought and yield penalty in cotton

BACKGROUND

Brassinosteroids (BRs) play crucial roles in drought tolerance, but the underlying molecular mechanisms remain unclear in the important oilseed and fiber crop, cotton (Gossypium hirsutum L.).

RESULTS

To elucidate how BRs mediate drought tolerance in cotton, a cotton brassinosteroid (BR)-deficient mutant, pag1 (pagoda1), was employed for analysis. Importantly, the pag1 mutant showed increased sensitivity to drought stress, with shorter primary roots and fewer lateral roots. The number of stomata was significantly increased in the mutant, and the stomata aperture was much wider than that of the control plants. These mutant plants therefore showed an increased water loss rate. Furthermore, the abscisic acid (ABA) content, photosynthetic efficiency and starch content of the mutant were significantly lower than those of the wild type. The overall performance of the mutant plants was worse than that of the wild-type control under both normal and drought conditions. Moreover, Proteomic analysis revealed reduced levels of stress-related proteins in pag1 plants.

CONCLUSIONS

These results suggest that BRs may modulate the drought tolerance of cotton by regulating much genes that related to drought stress and multiple organ responses to drought, including root growth, stomata development, the stomata aperture and photosynthesis. This study provides an important basis for understanding drought resistance regulated by BRs and cultivating drought-resistant cotton lines.

Mutation of ACX1, a Jasmonic Acid Biosynthetic Enzyme, Leads to Petal Degeneration in Chinese Cabbage (Brassica campestris ssp. pekinensis)

Petal color, size, and morphology play important roles in protecting other floral organs, attracting pollinators, and facilitating sexual reproduction in plants. In a previous study, we obtained a petal degeneration mutant (pdm) from the ‘FT’ doubled haploid line of Chinese cabbage and found that the candidate gene for pdm, Bra040093, encodes the enzyme acyl-CoA oxidase1. In this study, we sought to examine the gene networks regulating petal development in pdm plants. We show that the mRNA and protein expression of Bra040093, which is involved in the jasmonic acid (JA) biosynthetic pathway, were significantly lower in the petals of pdm plants than in those of ‘FT’ plants. Similarly, the JA and methyl jasmonate (MeJA) contents of petals were significantly lower in pdm plants than in ‘FT’ plants and we found that exogenous application of these hormones to the inflorescences of pdm plants restored the ‘FT’ phenotype. Comparative analyses of the transcriptomes of ‘FT’, pdm and pdm + JA (pJA) plants revealed 10,160 differentially expressed genes (DEGs) with consistent expression tendencies in ‘FT’ vs. pdm and pJA vs. pdm comparisons. Among these DEGs, we identified 69 DEGs related to floral organ development, 11 of which are involved in petal development regulated by JA. On the basis of qRT-PCR verification, we propose regulatory pathways whereby JA may mediate petal development in the pdm mutant. We demonstrate that mutation of Bra040093 in pdm plants leads to reduced JA levels and that this in turn promotes changes in the expression of genes that are expressed in response to JA, ultimately resulting in petal degeneration. These findings thus indicate that JA is associated with petal development in Chinese cabbage. These results enhance our knowledge on the molecular mechanisms underlying petal development and lay the foundations for further elucidation of the mechanisms associated with floral organ development in Chinese cabbage.