Related to ABI3 and VP1 (RAV) transcription factors belong to the AP2 and B3 superfamily.  RAVs genes have been reported to be involved in plant growth and development regulation.  This study screened three RAV genes from Medicago truncatula and named one of them MtRAV1.  The MtRAV1 overexpressing plants exhibits traits such as plant dwarfing, delayed flowering, reduced leaf and floral organs, increased branching, and reduced pods and seeds.  Gene expression analysis results showed that overexpression of MtRAV1 inhibited the expression of Flowering Locus T (MtFTa1), Suppressor of Overexpression of CO 1 (MtSOC1), GA3-oxidase1 (MtGA3OX1), DWARF14 (MtD14) and Carotenoid Cleavage Dioxygenase 7 (MtCCD7).  To further investigate the regulation pathway involved by MtRAV1, RNA-sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analysis were conducted.  RNA-seq results indicated that MtRAV1 might affect plant growth and development by regulating some genes in photosynthesis, circadian rhythm and plant hormone signaling pathways, especially the auxin signaling pathway.  Conjoint analysis of DAP-seq and RNA-seq revealed that MtRAV1 might inhibit the expression of Ferredoxin (MtFd-l3), Light-harvesting Chlorophyll a/b Binding Protein 1 (MtLhcb-l2) and Small Auxin Up-regulated RNA (MtSAUR-l), which related to photosystem II and auxin signaling pathway.  Summarily, MtRAV1 was preliminarily proven to be a key growth inhibitory factor in M. truncatula.

Oxidation of self-stored carbohydrates and lipids provides the energy for the rapid morphogenetic transformation during asexual and infection-related development in Pyricularia oryzae, which results in intracellular accumulation of reducing equivalents NADH and FADH₂, requiring a cytosolic shuttling machinery towards mitochondria.  Our previous studies identified the mitochondrial D-lactate dehydrogenase MoDld1 as a regulator to channel the metabolite flow in conjunction with redox homeostasis.  However, the regulator(s) facilitating the cytosolic redox balance and the importance in propelling nutrient metabolite flow remain unknown.  The G-3-P shuttle is a conserved machinery transporting the cytosolic reducing power to mitochondria.  In P. oryzae, the mitochondrial G-3-P dehydrogenase Gpd2 was required for cellular NAD⁺/NADH balance and fungal virulence.  In this study, we re-locate the mitochondrial G-3-P dehydrogenase Gpd2 to the cytosol for disturbing cytosolic redox status.  Our results showed overexpression of cytosolic gpd2^Δmts without the mitochondrial targeted signal (MTS) driven by Ribosomal protein 27 promoter (PR27) exerted conflicting regulation of cellular oxidoreductase activities compared to the ΔModld1 deletion mutant by RNA-seq and prevented the conidiation and pathogenicity of P. oryzae.  Moreover, overexpression of gpd2^Δmts caused defects in glycogen and lipid mobilization underlying asexual and infectious structural development associated with decreased cellular NADH production and weakened anti-oxidation activities.  RNA-seq and non-targeted metabolic profiling revealed down-regulated transcriptional activities of carbohydrate metabolism and lower abundance of fatty acids and secondary metabolites in RP27:gpd2^Δmts.  Thus, our studies indicate the essential role of cytosolic redox control in nutrient metabolism fueling the asexual and infection-related development in P. oryzae.

The seed storage materials accumulate during seed development, and are essential for seed germination and seedling establishment.  Here we employed two bi-parental populations of an F_2:3 population developed from a cross of improved 220 (I220, small seeds with low starch) and PH4CV (large seeds with high starch), as well as recombinant-inbred lines (RILs) of X178 (high starch) and its improved introgression line I178 (low starch), to identify the genes that control seed storage materials.  We identified a total of 12 QTLs for starch, protein and oil, which explained 3.44–10.79% of the phenotypic variances.  Among them, qSTA2-1 identified in F_2:3 and qSTA2-2 identified in the RILs partially overlapped at an interval of 7.314–9.554 Mb, and they explained 3.44–10.21% of the starch content variation, so they were selected for further study.  Fine mapping of qSTA2-2 with the backcrossed populations of I220/PH4CV in each generation narrowed it down to a 199.7 kb interval that contains 14 open reading frames (ORFs).  Transcriptomic analysis of developing seeds from the near-isogenic lines (NILs) of I220/PH4CV (BC₅F₂) showed that only 11 ORFs were expressed in 20 days after pollination (DAP) seeds.  Five of them were upregulated and six of them were downregulated in NIL^I220, and the differentially expressed genes (DEGs) between NIL^I220 and NIL^PH4CV were enriched in starch metabolism, hormone signal transduction and glycosaminoglycan degradation.  Of the eleven NIL^I220 differential expressed ORFs, ORF4 (Zm00001d002260) and ORF5 (Zm00001d002261) carry 75% protein sequence similarity, both encodes an glycolate oxidase, were the possible candidates of qSTA2-2.  Further analysis and validation indicated that mutation of the qSTA2-2 locus resulted in the dysfunction of ABA accumulation, the embryo/endosperm ratio and the starch and hormone levels.

The cAMP-dependent protein kinase A (PKA) signaling pathway has long been considered critical for long-term memory (LTM) formation.  Previous studies have mostly focused on the role of PKA signaling in LTM induction by multiple spaced conditioning with less attention to LTM induction by a single conditioning.  Here, we conducted behavioral-pharmacology, enzyme immunoassay and RNA interference experiments to study the role of the PKA signaling pathway in LTM formation in the agricultural pest Bactrocera dorsalis, which has a strong memory capacity allowing it to form a two-day memory even from a single conditioning trial.  We found that either blocking or activating PKA prior to conditioning pretreatment affected multiple spaced LTM, and conversely, they did not affect LTM formed by single conditioning.  This was further confirmed by enzyme-linked immunosorbent assay (ELISA) and silencing of the protein kinase regulatory subunit 2 and catalytic subunit 1.  Taken together, these results suggest that activating PKA during memory acquisition helps to induce the LTM formed by multiple spaced conditioning but not by a single conditioning.  Our findings challenge the conserved role of PKA signaling in LTM, which provides a basis for the greater diversity of molecular mechanisms underlying LTM formation across species, as well as possible functional and evolutionary implications.

Sugarcane/soybean intercropping with reduced nitrogen addition is an important sustainable agricultural pattern that can alter soil ecological functions, thereby affecting straw decomposition in the soil.  However, the mechanisms underlying changes in soil organic carbon (SOC) composition and microbial communities during straw decomposition under long-term intercropping with reduced nitrogen addition remain unclear.  In this study, we conducted an in-situ microplot incubation experiment with 13C-labeled soybean straw residue addition in a two-factor (cropping pattern: sugarcane monoculture (MS) and sugarcane/soybean intercropping (SB); nitrogen addition levels: reduced nitrogen addition (N1) and conventional nitrogen addition (N2)) long-term experimental field plot.  The results showed that the SBN1 treatment significantly increased the residual particulate organic carbon (POC) and residual microbial biomass carbon (MBC) contents during straw decomposition, and the straw carbon in soil was mainly conserved as POC.  Straw addition changed the structure and reduced the diversity of the soil microbial community, but microbial diversity gradually recovered with decomposition time.  During straw decomposition, the intercropping pattern significantly increased the relative abundances of Firmicutes and Ascomycota.  In addition, straw addition reduced microbial network complexity in the sugarcane/soybean intercropping pattern but increased it in the sugarcane monoculture pattern.  Nevertheless, microbial network complexity remained higher in the SBN1 treatment than in the MSN1 treatment.  In general, the SBN1 treatment significantly increased the diversity of microbial communities and the relative abundance of microorganisms associated with organic matter decomposition, and the changes in microbial communities were mainly driven by the residual labile SOC fractions.  These findings suggest that more straw carbon can be sequestered in the soil under sugarcane/soybean intercropping with reduced nitrogen addition to maintain microbial diversity and contribute to the development of sustainable agriculture.

Rice stripe disease, caused by rice stripe virus (RSV) which is transmitted by small brown planthopper (SBPH, Laodelphax striatellus Fallen), resulted in serious losses to rice production during the last 2 decades.  Research on the molecular differences between resistant and susceptible rice varieties and the interaction between rice and RSV remains inadequate.  In this study, RNA-Seq was used to analyze the transcriptomic differences between the resistant and susceptible rice varieties at different times post RSV infection.  Through Gene Ontology (GO) annotation, the differentially expressed genes (DEGs) related to transcription factors, peroxidases, and kinases of 2 varieties at 3 time points were identified.  Comparing these 2 varieties, the DEGs associated with these 3 GOs were numerically less in the resistant variety than in the susceptible variety, but the expression showed a significant up- or down-regulation trend under the conditions of |log₂(Fold change)|>0 & P_adj<0.05 by significance analysis.  Then through Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs involved in some pathways that have a contribution to disease resistance including plant hormone signal transduction and plant–pathogen interaction were found.  The results showed that resistance responses regulated by abscisic acid (ABA) and brassinosteroids (BR) were the same for 2 varieties, but that mediated by salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) were different.  The DEGs in resistant and susceptible varieties at the 3 time points were identified in both PAMP-triggered immunity (PTI) and Effector protein-triggered immunity (ETI), with that most of the unigenes of the susceptible variety were involved in PTI, whereas most of the unigenes of the resistant variety were involved in ETI.  These results revealed the different responses of resistant and susceptible varieties in the transcription level to RSV infection.

Cold stress is an important factor that limits apple production.  In this study, we examined the tissue-cultured plantlets of apple rootstocks ‘M9T337’ and ‘60-160’, which are resistant and sensitive to cold stress, respectively.  The enriched pathways of differentially expressed genes (DEGs) and physiological changes in ‘M9T337’ and ‘60-160’ plantlets were clearly different after cold stress (1°C) treatment for 48 h, suggesting that they have differential responses to cold stress.  The differential expression of WRKY transcription factors in the two plantlets showed that MdWRKY40is and MdWRKY48 are potential regulators of cold tolerance.  When we overexpressed MdWRKY40is and MdWRKY48 in apple calli, the overexpression of MdWRKY48 had no significant effect on the callus, while MdWRKY40is overexpression promoted anthocyanin accumulation, increased callus cold tolerance, and promoted the expression of anthocyanin structural gene MdDFR and cold-signaling core gene MdCBF2.  Yeast one-hybrid screening and electrophoretic mobility shift assays showed that MdWRKY40is could only bind to the MdDFR promoter.  Yeast two-hybrid screening and bimolecular fluorescence complementation showed that MdWRKY40is interacts with the CBF2 inhibitor MdMYB15L through the leucine zipper (LZ).  When the LZ of MdWRMY40is was knocked out, MdWRKY40is overexpression in the callus did not affect MdCBF2 expression or callus cold tolerance, indicating that MdWRKY40is acts in the cold signaling pathway by interacting with MdMYB15L.  In summary, MdWRKY40is can directly bind to the MdDFR promoter in order to promote anthocyanin accumulation, and it can also interact with MdMYB15L to interfere with its inhibitory effect on MdCBF2, indirectly promoting MdCBF2 expression, and thereby improving cold tolerance.  These results provide a new perspective for the cold-resistance mechanism of apple rootstocks and a molecular basis for the screening of cold-resistant rootstocks.

Indica hybrid rice (Oryza sativa) production aims to achieve two crucial targets: high yield and good taste.  This study selected three types of indica hybrid rice according to grain yield and taste value, including high yield and good taste (HYGT), low yield and good taste (LYGT), and high yield and poor taste (HYPT), to analyze yield components, corresponding growth characteristics, and rice taste quality.  When values were averaged across varieties and years, there were almost no differences in taste value between HYGT and LYGT; HYGT showed a significant increase in yield, owing to a higher number of panicles and spikelets per panicle, with a respective increment of 16.2 and 20.6%.  The higher grain yield of HYGT compared with LYGT was attributed to three key factors: a higher leaf area index (LAI) during heading, a higher ratio of grain to leaf, and a higher biomass accumulation at maturity.  HYGT and HYPT achieved similar high yields; however, HYGT had more panicle numbers and lower grain weight.  In addition, HYGT showed a significantly higher taste value than HYPT, attributed to its significantly lower protein and amylose contents, with reductions of 8.8 and 15.7%, respectively.  Lower protein and amylose contents might be caused by a proper matter translocation from vegetative organs to panicle.  This study suggested that reasonable panicle characteristics and translocation efficiency from vegetative organs to panicle during heading to maturity are the key factors in balancing yield and rice taste quality.  These results will provide valuable insights for rice breeders to improve the grain yield and quality of indica hybrid rice.

The fully mulched ridge–furrow (FMRF) system has been widely used on the semi-arid Loess Plateau of China due to its high maize (Zea mays L.) productivity and rainfall use efficiency.  However, high outputs under this system led to a depletion of soil moisture and soil nutrients, which reduces its sustainability in the long run.  Therefore, it is necessary to optimize the system for the sustainable development of agriculture.  The development, yield-increasing mechanisms, negative impacts, optimization, and their relations in the FMRF system are reviewed in this paper.  We suggest using grain and forage maize varieties instead of regular maize; mulching plastic film in autumn or leaving the mulch after maize harvesting until the next spring, and then removing the old film and mulching new film; combining reduced/no-tillage with straw return; utilizing crop rotation or intercropping with winter canola (Brassica campestris L.), millet (Setaria italica), or oilseed flax (Linum usitatissimum L.); reducing nitrogen fertilizer and partially replacing chemical fertilizer with organic fertilizer; using biodegradable or weather-resistant film; and implementing mechanized production.  These integrations help to establish an environmentally friendly, high quality, and sustainable agricultural system, promote high-quality development of dryland farming, and create new opportunities for agricultural development in the semi-arid Loess Plateau.

To achieve the dual goals of high yield and good quality with low environmental costs, slow-release fertilizer (SRF) has been widely used in lotus cultivation as new type of fertilizer instead of traditional nitrogen fertilizer.  However, the optimal amount of SRF and how it would promote lotus rhizome quality remain unclear.  This study was designed to investigate the photosynthetic characteristics and the synthesis, accumulation, and physicochemical properties of lotus rhizome starches under six SRF levels (CK, S1, S2, S3, S4, and S5).  Compared with CK (0 kg ha^–1), the net photosynthetic rate (P_n) and SPAD values of leaves remained at higher levels under SRF treatment.  Further research showed that SRF increased the lotus rhizome yield, the contents of amylose, amylopectin, and total starch, and the number of starch granules.  Among the six SRF levels, S3 (1 035 kg ha^–1) showed the greatest difference from CK and produced the highest levels.  With the increasing SRF levels, the peak, hot and final viscosities decreased at first and then increased, but the setback viscosity and pasting temperature increased.  In order to interpret these changes at the molecular level, the activities of key enzymes and relative expression levels of starch accumulation related genes were analyzed.  Each of these parameters also increased under SRF treatment, especially under the S3 treatment.  The results of this study show that SRF, especially S3 (1 035 kg ha^–1), is a suitable fertilizer option for lotus planting which can improve lotus rhizome quality by affecting starch accumulations related enzymes and genes.  These results will be useful for SRF application to high-quality lotus rhizome production with low environmental costs.

Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soil-borne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops.  Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology, although it cannot provide accurate transcript assembly and structural information.  In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R.  Overall, 39 376 high-quality isoforms and 26 270 open reading frames (ORFs) were identified from the SMRT sequencing data.  Additionally, 426 annotated long noncoding RNAs (lncRNAs), 56 transcription factor (TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing (AS) events were identified.  Furthermore, 1 201 of the genes had at least one AS event in DH40R.  A comparison with RNA-seq data revealed six differentially expressed AS genes (one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance.  The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.

The MADS-box (DAM) gene PpDAM6, which is related to dormancy, plays a key role in bud endodormancy release, and the expression of PpDAM6 decreases during endodormancy release.  However, the interaction network that governs its regulation of the endodormancy release of flower buds in peach remains unclear.  In this study, we used yeast two-hybrid (Y2H) assays to identify a mitogen-activated protein kinase, PpMAPK6, that interacts with PpDAM6 in a peach dormancy-associated SSHcDNA library.  PpMAPK6 is primarily located in the nucleus, and Y2H and bimolecular fluorescence complementation (BiFC) assays verified that PpMAPK6 interacts with PpDAM6 by binding to the MADS-box domain of PpDAM6.  Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of PpMAPK6 was opposite that of PpDAM6 in the endodormancy release of three cultivars with different chilling requirements (Prunus persica ‘Chunjie’, Prunus persica var. nectarina ‘Zhongyou 5’, Prunus persica ‘Qingzhou peach’).  In addition, abscisic acid (ABA) inhibited the expression of PpMAPK6 and promoted the expression of PpDAM6 in flower buds.  The results indicated that PpMAPK6 might phosphorylate PpDAM6 to accelerate its degradation by interacting with PpDAM6.  The expression of PpMAPK6 increased with decreasing ABA content during endodormancy release in peach flower buds, which in turn decreased the expression of PpDAM6 and promoted endodormancy release.

Agropyron cristatum (2n=4x=28, PPPP) is a wild relative of common wheat which contains a large number of desirable genes that can be exploited for wheat improvement.  Wheat–A. cristatum 2P alien translocation lines exhibit many desirable traits, such as small flag leaves, a high spikelet number and density, and a compact plant type.  An agronomic trait evaluation and a genetic analysis were carried out on translocation lines and backcross populations of these lines carrying different translocation fragments.  The results showed that a translocation fragment from 2PT-3 (2PL) reduced the length of the flag leaves, while translocation fragments from 2PT-3 (2PL) and 2PT-5 (2PL (0.60–1.00)) reduced the width of the flag leaves.  A translocation fragment from 2PT-13 (2PS (0.18–0.36)) increased the length and area of the flag leaves.  Translocation fragments from 2PT-3 (2PL) and 2PT-8 (2PL (0.86–1.00)) increased the density of spikelets.  Translocation fragments from 2PT-7 (2PL (0.00–0.09)), 2PT-8 (2PL (0.86–1.00)), 2PT-10 (2PS), and 2PT-13 (2PS (0.18–0.36)) reduced plant height.  This study provides a scientific basis for the effective utilization of wheat–A. cristatum translocation lines.