Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, is a destructive soil-borne disease leading to huge yield loss.  We previously reported that Klebsiella variicola FH-1 could degrade atrazine herbicides, and the vegetative growth of atrazine-sensitive crops (i.e., soybean) was significantly increased in the FH-1-treated soil.  Interestingly, we found that FH-1 could promote soybean growth and induce resistance to S. sclerotiorum.  In our study, strain FH-1 could grow in a nitrogen-free environment, dissolve inorganic phosphorus and potassium, and produce indoleacetic acid and a siderophore.  The results of pot experiments showed that K. variicola FH-1 promoted soybean plant development, substantially improving plant height, fresh weight, and root length, and induced resistance against S. sclerotiorum infection in soybean leaves.  The area under the disease progression curve (AUDPC) for treatment with strain FH-1 was significantly lower than the control and was reduced by up to 42.2% within 48 h (P<0.001).  Moreover, strain FH-1 rcovered the activities of catalase, superoxide dismutase, peroxidase, phenylalanine ammonia lyase, and polyphenol oxidase, which are involved in plant protection, and reduced malondialdehyde accumulation in the leaves.  The mechanism of induction of resistance appeared to be primarily resulted from the enhancement of transcript levels of PR10, PR12, AOS, CHS, and PDF1.2 genes.  The colonization of FH-1 on soybean root, determined using CLSM and SEM, revealed that FH-1 colonized soybean root surfaces, root hairs, and exodermis to form biofilms.  In summary, K. variicola FH-1 exhibited the biological control potential by inducing resistance in soybean against S. sclerotiorum infection, providing new suggestions for green prevention and control.

Anthocyanin is an important pigment that affects plant color and nutritional quality.  MYBs play an important role in plant anthocyanin synthesis and accumulation.  However, the regulatory function of MYB transcription factors in anthocyanin synthesis in flax flowers is still unclear.  In this study, 402 MYB transcription factors were identified in the flax genome.  These MYB members are unevenly distributed on 15 chromosomes.  The R2R3-LuMYB members were divided into 32 phylogenetic subfamilies.  qRT-PCR analysis showed that seven R2R3-LuMYB genes in the adjacent subfamily of the evolutionary tree had similar expression patterns, among which LuMYB216 was highly expressed in the petals of different colors.  Moreover, gene editing of LuMYB216 in flax showed that the petal color, anther color and seed coat color of mutant plants were significantly lighter than those of wild-type plants, and the anthocyanin content of lumyb216 mutant plants was significantly reduced.  Correlation analysis indicated that LuMYB216 was significantly positively correlated with the upstream regulator bHLH30.  This study systematically analyzed the MYB gene family in flax, laying a foundation for studying the regulation of LuMYB216 in flax flower anthocyanin synthesis.

Type I interferon (IFN-I) provides an important first line to protect avian species against pathogens invasion. IFN regulatory factor 7 (IRF7) has been identified as the most important regulator for both DNA and RNA virus-induced IFN-I production in chickens. Although four splicing variants of IRF7 have been identified in mammals, it is still unclear whether alternative splicing patterns and the function of IRF7 isoform(s) exist in chickens. In this study, we reported a novel short transcript isoform of chicken IRF7 (chIRF7), termed chIRF7-iso, which contained an intact N-terminal DNAbinding domain (DBD) and 14 amino acids different from chIRF7 in the C-terminal. Overexpression of chIRF7 in chicken leghorn male hepatocellular (LMH) cells activated the IFN-β promoter and significantly inhibited Newcastle disease virus (NDV) and fowl adenovirus serotype 4 (FAdV-4) replication. Conversely, overexpression of chIRF7-iso blocked the IFN-β promoter activity and was favorable for NDV and FAdV-4 replication in vitro. Collectively, our results confirm that a novel chIRF7 isoform-mediated negative regulates IFN-β production, which will contribute to understanding the role of chIRF7 in innate antiviral response in chicken.

Upland cotton (Gossypium hirsutum L.) is the most important natural textile fiber crop worldwide. Plant height (PH) is a significant component of plant architecture, strongly influencing crop cultivation patterns, overall yield, and economic coefficient. However, cotton genes regulating plant height have not been fully identified. Previously, an HD-Zip gene (GhHB12) was isolated and characterized in cotton, which regulates the abiotic and biotic stress responses and the growth and development processes. In this study, we showed that GhHB12 was induced by auxin. Moreover, overexpression of GhHB12 induces the expression of HY5, ATH1, and HAT4, represses the spatial-temporal distribution, polar transport, and signaling of auxin, alters the expression of genes involved in cell wall expansion, and restrains the plant height in cotton. These results suggest a role of GhHB12 in regulating cotton plant height, which could be achieved by affecting the auxin signaling and cell wall expansion.

In Bacillus thuringenesis (Bt) transgenic cotton, the cotton boll has the lowest insecticidal protein content when compared to the other organs.  The present study investigated the effects of amino acid spray application at the peak flowering stage on the cotton boll Bt toxin concentration and yield formation.  Boll protein synthesis and carbohydrate conversion were also studied to reveal the fundamental mechanism.  Three treatments (i.e., CK, the untreated control; LA1, five amino acids; LA2, 21 amino acids) were applied to two Bt cultivars of G. hirsutum (i.e., the hybrid Sikang 3 and the conventional Sikang 1) in the cotton-growing seasons during 2017 and 2018.  Amino acid spray application at the peak flowering stage resulted in an increase of 5.2–16.4% in the boll Bt protein concentration and an increase of 5.5–11.3% in the seed cotton yield, but there was no difference between the two amino acid treatments.  In addition, amino acid applications led to increases in the amino acid content, soluble protein content, glutamate pyruvate transaminase (GPT) activity, glutamate oxaloacetate transaminase (GOT) activity, glucose content, fructose content and soluble acid invertase (SAI) activity.  This study also found that Bt protein content, enhanced boll number and the weight of opened bolls were closely related to carbon and nitrogen metabolism.  The Bt protein content had significant linear positive correlations with amino acid and soluble protein contents.  Enhanced boll number had significant linear positive correlations with the GPT and GOT activities from 15–25 days after flowering (DAF).  The weight of opened bolls from 55–65 DAF had a significant linear positive correlation with the SAI activity.  These results indicate that the enhancement of boll protein synthesis and carbohydrate conversion by amino acid application resulted in a simultaneous increase in the boll Bt protein concentration and cotton lint yield.

Meloidogyne incognita is a devastating plant-parasitic nematode.  Effectors play important roles during the stages of nematodes infection and parasitism, but their molecular functions remain largely unknown.  In this study, we characterized a new effector, Minc03329, which contains signal peptide for secretion and a C-type lectin domain.  The yeast signal sequence trap experiments indicated that the signal peptide of Minc03329 is functional.  In situ hybridization showed that Minc03329 was specifically expressed in the subventral esophageal gland.  Real-time qPCR confirmed that the expression level of Minc03329 transcript was significantly increased in pre-parasitic and parasitic second-stage juveniles (pre-J2s and par-J2s).  Tobacco rattle virus (TRV)-mediated gene silencing of Minc03329 in host plants largely reduced the pathogenicity of nematodes.  On the contrary, ectopic expression of Minc03329 in Arabidopsis thaliana significantly increased plant susceptibility to nematodes.  Transient expression of Minc03329 in Nicotiana benthamiana leaves suppressed the programmed cell death triggered by the pro-apoptotic protein BAX.  Moreover, the transcriptome analysis of Minc03329-transgenic Arabidopsis and wild type revealed that many defense-related genes were significantly down-regulated.  Interestingly, some different expressed genes were involved in the formation of nematode feeding sites.  These results revealed that Minc03329 is an important effector for M. incognita, suppressing host defense response and promoting pathogenicity.

Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors.  In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice.  OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process.  OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein.  Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.  Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines.  Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay.  Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.

Soybean yield has been increased through high planting density, but investigating plant height and petiole traits to select for compact architecture, lodging resistance, and high yield varieties is an underexplored avenue to improve yield.  We compared the relationship between yield-related traits, lodging resistance, and petiole-associated phenotypes in the short petiole germplasm M657 with three control accessions over 2017-2018 in four locations of the Huang-Huai region.  The results showed M657 exhibited stable and high tolerance to high planting density and resistance to lodging, especially at the highest density (8×10⁵ plants ha^-1).  Regression analysis showed that shorter petiole length was significantly associated with increased lodging resistance.  Yield analysis showed that M657 achieved higher yields under higher densities, especially in the north Huang-Huai region.  There are markedly different responses to intra- and inter-row spacing designs among varieties in both lodging and yield related to location and density.  Lodging was positively correlated with planting density, plant height, petiole length, and number of effective branches, and negatively correlated with stem diameter, seed number per plant, and seed weight per plant.  The yield of soybean was increased by appropriately increasing planting density on the basis of current soybean varieties in the Huang-Huai region.  This study provides a valuable new germplasm resource for introgression of compact architecture traits amenable to high yield in high density planting systems and establishes a high-yield model of soybean in the Huang-Huai region.

Improving soil quality while achieving higher productivity is the major challenge in the agricultural industry.  Wheat (Triticum aestivum L.)–maize (Zea mays L.) (W–M) rotation is the dominant planting pattern in the Huang-Huai-Hai  Plain and is important for food security in China.  However, the soil quality is deteriorating due to the W–M rotation’s long-term, intensive, and continuous cultivation.  Introducing legumes into the W–M rotation system may be an effective way to improve soil quality.  In this study, we aimed to verify this hypothesis by exploring efficient planting systems (wheat–peanut (Arachis hypogaea L.) (W–P) rotation and wheat rotated with maize and peanut intercropping (W–M/P)) to achieve higher agricultural production in the Huang-Huai-Hai   Plain.  Using traditional W–M rotation as the control, we evaluated crop productivity, net returns, soil microorganisms (SMs), and soil organic carbon (SOC) fractions for three consecutive years.  The results indicated that wheat yields were significantly increased under W–P and W–M/P (382.5–579.0 and 179.8–513.1 kg ha⁻¹, respectively) compared with W–M.  W–P

and W–M/P provided significantly higher net returns (58.2 and 70.4%, respectively) than W–M.  W–M/P and W–M retained the SOC stock more efficiently than W–P, increasing by 25.46–31.03 and 14.47–27.64%, respectively, in the 0–20 cm soil layer.  Compared with W–M, W–M/P improved labile carbon fractions; the sensitivity index of potentially mineralizable carbon, microbial biomass carbon (MBC), and dissolved organic carbon was 31.5, 96.5–157.2, and 17.8% in 20–40, 10–40, and 10–20 cm soil layers, respectively.  The bacterial community composition and bacteria function were altered as per the soil depth and planting pattern.  W–M/P and W–M exhibited similar bacterial community composition and function in 0–20 and 20–40 cm soil layers.  Compared with W–P, a higher abundance of functional genes, namely, contains mobile elements and stress-tolerant, and a lower abundance of genes, namely, potentially pathogenic, were observed in the 10–20 cm soil layer of W–M and the 0–20 cm soil layer of W–M/P.  SOC and MBC were the main factors affecting soil bacterial communities, positively correlated with Sphingomonadales and Gemmatimonadales and negatively correlated with Blastocatellales.  Organic input was the main factor affecting SOC and SMs, which exhibited feedback effects on crop productivity.  In summary, W–M/P improved productivity, net returns, and SOC pool compared with traditional W–M rotation systems, and it is recommended that plant–soil–microbial interactions be considered while designing high-yield cropping systems.

Tea is one of the most popular non-alcoholic beverages in the world, and free amino acids, especially theanine, make a major contribution to the umami taste of tea.  However, the genetic basis of the variation in amino acid content in tea plants remains largely unknown.  Here, we measured the free amino acid content in fresh leaves of 174 tea accessions over two years using a targeted metabolomics approach and obtained genotype data via RNA sequencing.  Genome-wide association studies were conducted to investigate loci affecting the content of free amino acids.  A total of 69 quantitative trait loci (–log₁₀(P-value)>5) were identified.  Functional annotation revealed that branched-chain amino acid aminotransferase, glutamine synthetase, nitrate transporter, and glutamate decarboxylase might be important for amino acid metabolism.  Two significant loci, glutamine synthetase (Glu1, P=3.71×10^–4; Arg1, P=4.61×10^–5) and branched-chain amino acid aminotransferase (Val1, P=4.67×10^–5; I_Leu1, P=3.56×10^–6), were identified, respectively.  Based on the genotyping result, two alleles of CsGS (CsGS-L and CsGS-H) and CsBCAT (CsBCAT-L and CsBCAT-H) were selected to perform function verification.  Overexpression of CsGS-L and CsGS-H enhanced the contents of glutamate and arginine in transgenic plants, and overexpression of CsBCAT-L and CsBCAT-H promoted the accumulation of valine, isoleucine and leucine.  Enzyme activity assay uncovered that SNP₁₀₅₄ is important for CsGS catalyzing glutamate into glutamine.  Furthermore, CsGS-L and CsGS-H differentially regulated the accumulation of glutamine, and CsBCAT-L and CsBCAT-H differentially regulated the accumulation of branched-chain amino acids.  In summary, the findings in our study would provide new insights into the genetic basis of amino acids contents variation in tea plants and facilitate the identification of elite genes to enhance amino acids content.

Sex determination in plants gives rise to unisexual flowers.  A better understanding of the regulatory mechanism underlying the production of unisexual flowers will help to clarify the process of sex determination in plants and allow researchers and farmers to harness heterosis.  Androecious cucumber (Cucumis sativus L.) plants can be used as the male parent when planted alongside a gynoecious line to produce heterozygous seeds, thus reducing the cost of seed production.  The isolation and characterization of additional androecious genotypes in varied backgrounds will increase the pool of available germplasm for breeding.  Here, we discovered an androecious mutant in a previously generated ethyl methanesulfonate (EMS)-mutagenized library of the cucumber inbred line ‘406’.  Genetic analysis, whole-genome resequencing, and molecular marker-assisted verification demonstrated that a nonsynonymous mutation in the ethylene biosynthetic gene 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 11 (ACS11) conferred androecy.  The mutation caused an amino acid change from serine (Ser) to phenylalanine (Phe) at position 301 (S301F).  In vitro enzyme activity assays revealed that this S301F mutation leads to a complete loss of enzymatic activity.  This study provides a new germplasm for use in cucumber breeding as the androecious male parent, and it offers new insights into the catalytic mechanism of ACS enzymes.

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.

Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes.  During early development, a population of skeletal muscle satellite cells (SSCs) proliferate into myoblasts.  The myoblasts then undergo further differentiation and fusion events, leading to the development of myotubes.  However, the mechanisms involved in the transition from SSCs to myotube formation remain unclear.  In this study, we characterized changes in the proteomic and transcriptomic expression profiles of SSCs, myoblasts (differentiation for 2 d) and myotubes (differentiation for 10 d).  Proteomic analysis identified SLMAP and STOM as potentially associated with myotube formation.  In addition, some different changes in MyoD, MyoG, Myosin7 and Desmin occurred after silencing SLMAP and STOM, suggesting that they may affect changes in the myogenic marker.  GO analysis indicated that the differentiation and migration factors SVIL, ENSCHIG00000026624 (AQP1) and SERPINE1 enhanced the transition from SSCs to myoblasts, accompanied by changes in the apoptotic balance.  In the myoblast vs. myotube group, candidates related to cell adhesion and signal transduction were highly expressed in the myotubes.  Additionally, CCN2, TGFB1, MYL2 and MYL4 were identified as hub-candidates in this group.  These data enhance our existing understanding of myotube formation during early development and repair.

Phenotypic screening of soybean germplasm suitable for high planting density is currently the most viable strategy to increase yield.  Previous studies have shown that soybean varieties with dwarf features and a short petiole often exhibit a compact plant architecture which could improve yield through increased planting density, although previously reported short petiole accessions were ultimately not usable for breeding in practice.  Here, we established a method to assess petiole length and identified an elite mutant line, M657, that exhibits high photosynthetic efficiency.  The agronomic traits of M657 were evaluated under field conditions, and appeared to be stable for short petiole across seven locations in northern, Huang–Huai, and southern China from 2017 to 2018.  Compared with the Jihuang 13 wild type, the mutant M657 was shorter in both petiole length and plant height, exhibited lower total area of leaf, seed weight per plant and 100-seed weight, but had an increased number of effective branches and the growth period was prolonged by 2–7 days.  Using M657 as a parental line for crosses with four other elite lines, we obtained four lines with desirable plant architecture and yield traits, thus demonstrating the feasibility of adopting M657 in breeding programs for soybean cultivars of high density and high yield.

Soft rot caused by Pectobacterium carotovorum (Pc) is a devastating disease of Brassica rapa, causing substantial reductions in crop yield and quality.  Identifying genes related to soft rot resistance is the key to solving this problem.  To characterize soft rot resistance, we screened a soft rot-susceptible Chinese cabbage (A03), a resistant pakchoi (‘Huaguan’), and a resistant mutant (sr).  An F₂ population was generated by crossing susceptible Chinese cabbage A03 and resistant pakchoi ‘Huaguan’ to identify quantitative trait loci (QTLs) that confer soft rot resistance.  A high-density genetic map was constructed and the three QTLs identified contain 166 genes.  Based on available transcriptome data, we analyzed the expression of the 166 genes during an important defense regulatory period in Pc infection in both A03 and the resistant mutant sr.  Among the 166 genes, six candidate genes were related to the soft rot defense response in B. rapa.  TIFY10B (JAZ2, BraA07g038660.3C) was located in the major soft rot resistance QTL, DRQTL-3 on A07, and we speculate that this gene may play an important role in the defense mechanism against soft rot in B. rapa.  This study lays the foundation for further investigations on the mechanism of soft rot resistance in B. rapa crops.

Legume cultivars affect N uptake, component crop growth, and soil physical and chemical characteristics in maize–legume intercropping systems.  However, how belowground interactions mediate root growth, N fixation, and nodulation of different legumes to affect N uptake is still unclear.  Hence, a two-year experiment was conducted with five planting patterns, i.e., maize–soybean strip intercropping (IMS), maize–peanut strip intercropping (IMP), and corresponding monocultures (monoculture maize (MM), monoculture soybean (MS), and monoculture peanut (MP)), and two N application rates, i.e., no N fertilizer (N–) and conventional N fertilizer (N+), to examine relationships between N uptake and root distribution of crops, legume nodulation and soil N availability.  Results showed that the averaged N uptake per unit area of intercrops was significantly lower than the corresponding monocultures.  Compared with the monoculture system, the N uptake of the intercropping systems increased by 31.7–45.4% in IMS and by 7.4–12.2% in IMP, respectively.  The N uptake per plant of intercropped maize and soybean significantly increased by 61.6 and 31.8%, and that of intercropped peanuts significantly decreased by 46.6% compared with the corresponding monocultures.  Maize and soybean showed asymmetrical distribution of roots in strip intercropping systems.  The root length density (RLD) and root surface area density (RSAD) of intercropped maize and soybean were significantly greater than that of the corresponding monocultures.  The roots of intercropped peanuts were confined, which resulted in decreased RLD and RSAD compared with the monoculture.  The nodule number and nodule fresh weight of soybean were significantly greater in IMS than in MS, and those of peanut were significantly lower in IMP than in MP.  The soil protease, urease, and nitrate reductase activities of maize and soybean were significantly greater in IMS and IMP than in the corresponding monoculture, while the enzyme activities of peanut were significantly lower in IMP than in MP.  The soil available N of maize and soybean was significantly greater increased in IMS and IMP than in the corresponding monocultures, while that of IMP was significantly lower than in MP.  In summary, the IMS system was more beneficial to N uptake than the IMP system.  The intercropping of maize and legumes can promote the N uptake of maize, thus reducing the need for N application and improving agricultural sustainability.

OVATE family proteins (OFPs) are plant-specific proteins with a conserved OVATE domain that regulate plant growth and development.  Although OFPs have been studied in several species, their biological functions remain largely unknown in cucumber (Cucumis sativus L.).  This study identified 19 CsOFPs distributed on seven chromosomes in cucumber.  Most CsOFP genes were expressed in reproductive organs, but with different expression patterns.  Ectopic expression of CsOFP12-16c in Arabidopsis resulted in shorter and blunt siliques.  The overall results indicated that CsOFP12-16c regulates silique development in Arabidopsis and may have a similar function in cucumber.

Soil biotic communities play vital roles in enhancing soil nutrient cycling and soil fertility.  Long-term excessive nitrogen (N) application is disadvantageous to the stability of soil food webs and affects arable soil health and sustainable utilization.  Proper organic substitution is essential to improve soil health and alleviate the disadvantages of excessive chemical fertilization.  However, the biological effects of various organic amendments on soil micro-food webs are poorly understood.  In order to explore the effects of various organic amendments including stover, biochar and manure on soil micro-food webs (microbial and nematode communities), a field plot experiment with maize having five treatments viz., 100% urea (100% N), 70% urea (70% N), 70% urea plus stover (Stover), 70% urea plus cattle manure (Manure) and 70% urea plus biochar (Biochar) was conducted.  Manure treatment increased the carbon (C) to N use efficiency of soil microbes, which contributed to the retention of soil C, while Biochar treatment elevated soil organic C (SOC) and soil pH.  Additionally, Biochar treatment mitigated the negative effects of soil acidification on the soil micro-food web and reduced the abundance of plant parasites.  Overall, the biological effect of organic amendments was distinguished from chemical fertilization (100% N and 70% N) through principal co-ordinates analysis.  Negative relationships among soil properties, microbial and nematode biomass in the 100% N treatment were diminished in treatments where chemical fertilizer was reduced.  The bottom-up effects on soil food webs were observed in organic substitution treatments.  In conclusion, organic amendments improved soil fertility by regulating soil microbial and nematode communities in the cropland ecosystem, alleviated the negative effects of chemical fertilizer on the micro-food webs and controlled the trophic cascades among soil biota.