Lilium are highly economically valuable ornamental plants that are susceptible to Fusarium wilt caused by Fusarium oxysporum. Lilium regale Wilson, a wild lily native to China, is highly resistant to F. oxysporum. In this study, a WRKY transcription factor, WRKY11, was isolated from L. regale, and its function during the interaction between L. regale and F. oxysporum was characterized. The resistance to F. oxysporum of LrWRKY11 ectopic expression tobacco increased, moreover, the transcriptome sequencing and UHPLC-MS/MS analysis indicated that the methyl salicylate and methyl jasmonate levels rose in LrWRKY11 transgenic tobacco, meanwhile, the expression of lignin/lignans biosynthesis related genes including a dirigent (DIR) were up-regulated. Moreover, the lignin/lignans contents in LrWRKY11 transgenic tobacco also significantly increased compared with the wild-type tobacco. In addition, the resistance of L. regale scales in which LrWRKY11 expression was silenced by RNAi evidently decreased, and additionally, the expression of lignin/lignans biosynthesis related genes including LrDIR1 was significantly suppressed. Therefore, LrDIR1 and its promoter (PLrDIR1) sequence containing the W-box element were isolated from L. regale. The interaction assay indicated that LrWRKY11 specifically bound to the W-box element in PLrDIR1 and activated LrDIR1 expression. Additionally, β-glucuronidase activity in the transgenic tobacco co-expressing LrWRKY11/PLrDIR1-β-glucuronidase was higher than that in transgenic tobacco expressing PLrDIR1-β-glucuronidase alone. Furthermore, the ectopic expression of LrDIR1 in tobacco enhanced the resistance to F. oxysporum and increased the lignin/lignans accumulation. In brief, this study revealed that LrWRKY11 positively regulated L. regale resistance to F. oxysporum through interaction with salicylic acid/jasmonic acid signaling pathways and modulating LrDIR1 expression to accumulate lignin/lignans.

Nitrogen, phosphorus, and potassium are essential macronutrients crucial not only for maize growth and development, but also for crop yield and quality.  The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown.  In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination.  We then calculated conditional phenotypic values at different time intervals to explore dynamic characteristics of N, P, and K concentrations. Abundant phenotypic variation was observed in the concentration and net changes of these nutrients.  Unconditional quantitative trait locus (QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for N, P, and K concentrations, respectively.  Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in N, P, and K concentrations.  By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for N, P, and K concentration, respectively, including GRMZM2G371058 encoding a Dof-type zinc finger DNA-binding family protein, associated with N concentration, and GRMZM2G113967 encoding a CBL-interacting protein kinase, related to K concentration.  Our results should deepen understanding of genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for genetic improvement of nutrient concentrations in maize.

The two-spotted spider mite, Tetranychus urticae Koch, is one of the most harmful pests in many agroecosystems worldwide. To effectively manage this pest, there is an urgent need to develop novel bio-active acaricides that support integrated pest management strategies targeting T. urticae. In this study, we explored the acaricidal effects of xenocoumacin 1 (Xcn1) on T. urticae and its predator Neoseiulus californicus using the highly purified compound. Xcn1 was extracted and purified from the cell-free supernatant of the Xenorhabdus nematophila CB6 mutant constructed by the easy promoter activated compound identification (easyPACId) method. When the concentration of Xcn1 exceeded 100 μg mL^-1, the survival rate of spider mite adults declined to below 40% and the fecundity was decreased by 80% at six days post application. At concentrations of 25 and 50 μg mL^-1, Xcn1 significantly impeded spider mite development by inhibiting the molt. However, neither concentration had any adverse effects on the survival or reproduction of the predatory mite N. californicus. The results from laboratory and semifield experiments consistently demonstrated the effectiveness of the antimicrobial metabolite Xcn1 in controlling pest mites at both the molecular and physiological levels. Our study offers a promising possibility that combines the compatible biocontrol agents of Xcn1 and predatory mites for integrated pest mite control.

α-Linolenic acid (ALA, 18:3Δ9,12,15) is an essential fatty acid for human, since it is the precursor for the biosynthesis of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA).  Modern people generally suffer from deficiency of ALA, since most staple food oils are low or lack in ALA content.  Biotechnological enrichment of ALA in staple oil crops is a promising strategy.  Among known oil crops, chia (Salvia hispanica) has the highest ALA content in its seed oil.  In this study, the FAD2 and FAD3 genes from chia were engineered into a staple oil crop, oilseed rape (Brassica napus), via Agrobaterium tumefaciens-mediated transformation of their LP4-2A fusion gene construct driven by the seed-specific promoter P_NapA.  In seeds of T0, T1 and T2 lines, the average ALA contents were 20.86, 23.54 and 24.92%, which were 2.21, 2.68 and 3.03 folds of the non-transformed controls (9.42, 8.78 and 8.22%), respectively.  The highest ALA levels of seeds of T0, T1 and T2 plants, were 38.41, 35.98 and 39.19% respectively, which were 4.10-4.77 folds of the respective controls.  FA-pathway enzyme genes BnACCD, BnFATA, BnSAD, BnSCD, BnDGAT1, BnDGAT2 and BnDGAT3 as well as positive regulatory genes BnWRI1, BnLEC1, BnL1L, BnLEC2, BnABI3, BnbZIP67 and BnMYB96 were all significantly up-regulated.  In contrast, BnTT1, BnTT2, BnTT8, BnTT16, BnTTG1 and BnTTG2, encoding negative regulators of oil accumulation but positive regulators of secondary metabolism, were all significantly down-regulated.  These mean that foreign ShFAD2-ShFAD3 fusion gene directly and indirectly remodeled both positive and negative loci of the whole FA-related network in transgenic B. napus seeds.

The development of receptive endometrium (RE) from pre-receptive endometrium (PE) for successful embryo implantation is a complex dynamic process in which the morphology and physiological states of the endometrial epithelium undergo a series of significant changes, including cell proliferation and apoptosis. However, the molecular mechanisms are not yet fully understood. In this study, a higher circRNA3669 level was observed in PE than in RE of goats. Functional assays revealed that this overexpression promoted the proliferation of goat endometrial epithelial cells (GEECs) by activating the expression of genes related to the PI3K/AKT-mTOR and MAPK pathways, thereby inhibiting apoptosis in vitro. Furthermore, circRNA3669 functioned as a competing endogenous RNA (ceRNA) to upregulate Reticulocalbin-2 (RCN2) expression at the post-transcriptional level by interacting with and downregulating miR-26a in GEECs. In addition, RCN2, which is highly expressed in the PE of goats, was found to be regulated by β-estradiol (E2) and progesterone (P4). Our results demonstrated that RCN2 also affected the key proteins PI3K, AKT, mTOR, JNK, and P38 in the PI3K/AKT-mTOR and MAPK pathways, thereby facilitating GEECs proliferation and suppressing their apoptosis in vitro. Collectively, we constructed a new circRNA3669-miR-26a-RCN2 regulatory network in GEECs, which further provides strong evidence that circRNA could potentially play a crucial regulatory role in the development of RE in goats. 

Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.  However, the molecular mechanism driving AsA richness in fruit remains unclear.  In order to reveal the molecular mechanism of AsA richness in A. eriantha, this study constructed a regulatory network related to AsA metabolism by combining genomics, metabolomics and transcriptomics.  We assembled a high-quality genome of A. eriantha ‘Ganlv 1’ with only five remaining gaps.  The assembly is comprised of 29 pseudochromosomes with a total size of 615.95 Mb, and contig N50 of 20.35 Mb. Among them, 24 of the pseudochromosomes were obtained directly from telomere-to-telomere.  The LTR assembly index score and consensus quality value were 21.34 and 39.90%, respectively.  Subsequently, 61 metabolites and 2 092 genes were found to be differentially accumulated/expressed during fruit development by metabolome and transcriptome assays, respectively.  AsA metabolism and the cyclic regeneration pathway were found to have high expression levels throughout fruit growth and development, suggesting its crucial role in the regulation of AsA.  Furthermore, the AsA contents are highly associated with ascorbate peroxidase genes.  The genome obtained in this study provides genomic resources for the genetic and breeding research of A. eriantha, and the constructed regulatory network can provide a public data platform for future research on kiwifruit.

The paper reviews studies of rural transformation in three dimensions – definition, measurement, and indicators – and summarises the findings of rural transformation research. The scope of rural transformation includes four elements – productivity, rurality, inclusiveness, and sustainability. Current concepts of the dimensions of rural transformation and their associated indicators are insufficient for policy decision-making, as they lack objectivity, feasibility, accountability, comprehensiveness, and comparability. Future research to develop new measures to assess rural transformation in developing countries is valuable. Furthermore, there is potential to explore the topic in some directions: urbanisation strategy, public intervention (i.e., institution, policy, and investment), gender inclusiveness, market creation, and international trade.

The practice of intercropping leguminous and gramineous crops is used for promoting sustainable agriculture, optimizing resource utilization, enhancing biodiversity, and reducing reliance on petroleum products.  However, promoting conventional intercropping strategies in modern agriculture can prove challenging.  The innovative technology of soybean maize strip intercropping (SMSI) has been proposed as a solution.  This system has produced remarkable results in improving domestic soybean and maize production for both food security and sustainable agriculture.  In this article, we provide an overview of SMSI and explain how it differs from traditional intercropping.  We also discuss the core principles that foster higher yields and the prospects for its future development.

Citrus yellow mottle-associated virus (CiYMaV) belonging to the subgenus Mandarivirus within the genus Potexvirus, was first identified in 2018 from Pakistan (CiYMaV-PK), where it is endemic in several regions.  Here, three full-length cDNA clones (pCiYMaV-FL-1, pCiYMaV-FL-18, and pCiYMaV-FL-22) corresponding to the genomic RNA of CiYMaV were constructed and then agroinfiltrated on Chandler pummelo (Citrus grandis) seedlings using the vacuum infiltration method.  All the inoculated plants developed severe vein yellowing, leaf mottling, and dwarfing symptoms by 40 days post-infiltration (dpi).  The results of a direct tissue blot immunoassay and reverse transcription polymerase chain reaction detection showed 94.7–100% infection rates of pCiYMaV-FL at 60 dpi.  Despite there being no observed difference among the three clones in the severity of symptom, pCiYMaV-FL-22 showed the highest accumulation levels of viral RNA and coat proteins.  Moreover, pCiYMaV-FL-22 successfully infected seven other citrus varieties and induced symptoms in five of them.  Transmission electron microscopy identified the presence of filamentous virus particles in extracts from systemic leaves of the plants infected with pCiYMaV-FL-22 at 6-months post-infiltration.  Taken together, the results indicate that Koch’s postulates were fulfilled for CiYMaV in citrus plants.  This is the first report of full-length infectious cDNA clones of CiYMaV, and thus, the data provide a basis for further study of the molecular mechanisms of virus infection and the development of a viral vector to express foreign genes in citrus plants.

Avian infectious bronchitis (IB) is a highly contagious infectious disease caused by infectious bronchitis virus (IBV), which is prevalent in many countries worldwide and causes serious harm to the poultry industry.  At present, many commercial IBV vaccines have been used for the prevention and control of IB; however, IB outbreaks occur frequently.  In this study, two new strains of IBV, SX/2106 and SX/2204, were isolated from two flocks which were immunized with IBV H120 vaccine in central China.  Phylogenetic and recombination analysis indicated that SX/2106, which was clustered into the GI-19 lineage, may be derived from recombination events of the GI-19 and GI-7 strains and the LDT3-A vaccine.  Genetic analysis showed that SX/2204 belongs to the GVI-1 lineage, which may have originated from the recombination of the GI-13 and GVI-1 strains and the H120 vaccine.  The virus cross-neutralization test showed that the antigenicity of SX/2106 and SX/2204 was different from H120.  Animal experiments found that both SX/2106 and SX/2204 could replicate effectively in the lungs and kidneys of chickens and cause disease and death, and H120 immunization could not provide effective protection against the two IBV isolates.  It is noteworthy that the pathogenicity of SX/2204 has significantly increased compared to the GVI-1 strains isolated previously, with a mortality rate up to 60%.  Considering the continuous mutation and recombination of the IBV genome to produce new variant strains, it is important to continuously monitor epidemic strains and develop new vaccines for the prevention and control of IBV epidemics.

Sugar is an indispensable source of energy for plant growth and development, and it requires the participation of sugar transporter proteins (STPs) for crossing the hydrophobic barrier in plants.  Here, we systematically identified the genes encoding sugar transporters in the genome of maize (Zea mays L.), analyzed their expression patterns under different conditions, and determined their functions in disease resistance.  The results showed that the mazie sugar transporter family contained 24 members, all of which were predicted to be distributed on the cell membrane and had a highly conserved transmembrane transport domain.  The tissue-specific expression of the maize sugar transporter genes was analyzed, and the expression level of these genes was found to be significantly different in different tissues.  The analysis of biotic and abiotic stress data showed that the expression levels of the sugar transporter genes changed significantly under different stress factors.  The expression levels of ZmSTP2 and ZmSTP20 continued to increase following Fusarium graminearum infection.  By performing disease resistance analysis of zmstp2 and zmstp20 mutants, we found that after inoculation with Cochliobolus carbonum, Setosphaeria turcica, Cochliobolus heterostrophus, and F. graminearum, the lesion area of the mutants was significantly higher than that of the wild-type B73 plant.  In this study, the genes encoding sugar transporters in maize were systematically identified and analyzed at the whole genome level.  The expression patterns of the sugar transporter-encoding genes in different tissues of maize and under biotic and abiotic stresses were revealed, which laid an important theoretical foundation for further elucidation of their functions.

Land use influences soil biota community composition and diversity, and then belowground ecosystem processes and functions. To characterize the effect of land use on soil biota, soil nematode communities in crop land, forest land and fallow land were investigated in six regions of northern China. Generic richness, diversity, abundance and biomass of soil nematodes was the lowest in crop land. The richness and diversity of soil nematodes were 28.8 and 15.1% higher in fallow land than in crop land, respectively. No significant differences in soil nematode indices were found between forest land and fallow land, but their network keystone genera composition was different. Among the keystone genera, 50% of forest land genera were omnivores-predators and 36% of fallow land genera were bacterivores. The proportion of fungivores in forest land was 20.8% lower than in fallow land. The network complexity and the stability were lower in crop land than forest land and fallow land. Soil pH, NH₄⁺-N and NO₃^--N were the major factors influencing the soil nematode community in crop land while soil organic carbon and moisture were the major factors in forest land. Soil nematode communities in crop land influenced by artificial management practices were more dependent on the soil environment than communities in forest land and fallow land. Land use induced soil environment variation and altered network relationships by influencing trophic group proportions among keystone nematode genera. 

Canopy temperature, which strongly influences crop yield formation, is closely related to plant physiological traits.  However, the effects of nitrogen treatment on canopy temperature and rice growth have not been comprehensively examined.  We conducted a two-year field experiment with three rice varieties (HD-5, NJ-9108, and YJ-805) and three nitrogen treatments (i.e., zero-N control (CK), 200 kg ha^–1 (MN), and 300 kg ha^–1 (HN)).  We measured canopy temperature using a drone equipped with a high-precision camera at the six stages of the growth period.  Generally, canopy temperature was found to be significantly higher for CK than for MN and HN during the tillering, jointing, booting, and heading stages.  The temperature was not found to be significantly different among the nitrogen treatments between the milky and waxy stages.  The canopy temperature of different rice varieties was found to follow the order: HD-5>NJ-9108>YJ-805, but the difference was not significant.  The canopy temperature of rice was mainly related to plant traits, such as shoot fresh weight (correlation coefficient r=-0.895), plant water content (-0.912), net photosynthesis (-0.84), stomatal conductance (-0.91), transpiration rate (-0.90), and leaf stomatal area (-0.83).  A structural equation model (SEM) showed that nitrogen fertilizer was an important factor affecting the rice canopy temperature.  Our study revealed that: (1) a suite of plant traits was associated with the nitrogen effects on canopy temperature, (2) the heading stage was the best time to observe rice canopy temperature, and (3) at that stage, canopy temperature was negatively correlated with rice yield, panicle number, and grain number per panicle.  This study provides that canopy temperature may be a convenient and accurate indicator of rice growth and yield prediction.

Numbers of vertebrae is an important economic trait associated with body size and meat productivity in animals.  However, the genetic basis of vertebrae number in donkey remains to be well understood.  The aim of this study was to identify candidate genes affecting the number of thoracic (TVn) and the number of lumbar vertebrae (LVn) in Dezhou donkey.  A genome-wide association study was conducted using whole genome sequence data imputed from low-coverage genome sequencing.  For TVn, we identified 38 genome-wide significant and 64 suggestive SNPs, which relate to 7 genes (NLGN1, DCC, SLC26A7, TOX, WNT7A, LOC123286078, and LOC123280142).  For LVn, we identified 9 genome-wide significant and 38 suggestive SNPs, which relate to 8 genes (GABBR2, FBXO4, LOC123277146, LOC123277359, BMP7, B3GAT1, EML2, and LRP5).  The genes involve in the Wnt and TGF-β signaling pathways and may play an important role in embryonic development or bone formation and could be good candidate genes for TVn and LVn.

Enhancing photosynthetic efficiency is a major goal for improving crop yields under agricultural field conditions and is associated with chloroplast biosynthesis and development.  In this study, we demonstrate that Golden2-like 1a (BnGLK1a) plays an important role in regulating chloroplast development and photosynthetic efficiency.  Overexpressing BnGLK1a resulted in significant increases in chlorophyll content, the number of thylakoid membrane layers and photosynthetic efficiency in Brassica napus, while knocking down BnGLK1a transcript levels through RNA interference (RNAi) had the opposite effects.  A yeast two-hybrid screen revealed that BnGLK1a interacts with the abscisic acid receptor PYRABACTIN RESISTANCE 1-LIKE 1–2 (BnPYL1–2) and CONSTITUTIVE PHOTOMORPHOGENIC 9 SIGNALOSOME 5A subunit (BnCSN5A), which play essential roles in regulating chloroplast development and photosynthesis.  Consistent with this, BnGLK1a-RNAi lines of B. napus display hypersensitivity to the abscisic acid (ABA) response.  Importantly, overexpression of BnGLK1a resulted in a 10% increase in thousand-seed weight, whereas seeds from BnGLK1a-RNAi lines were 16% lighter than wild type.  We propose that BnGLK1a could be a potential target in breeding for improving rapeseed productivity.  Our results not only provide insights into the mechanisms of BnGLK1a function, but also offer a potential approach for improving the productivity of Brassica species.

Bacteria play critical roles in regulating soil phosphorus (P) cycling.  The effects of interactions between crops and soil P-availability on bacterial communities and the feedback regulation of soil P cycling by the bacterial community modifications are poorly understood.  Here, six soybean (Glycinemax) genotypes with differences in P efficiency were cultivated in acidic soils with long-term sufficient or deficient P-fertilizer treatments.  The acid phosphatase (AcP) activities, organic-P concentrations and associated bacterial community compositions were determined in bulk and rhizosphere soils.  The results showed that both soybean plant P content and the soil AcP activity were negatively correlated with soil organic-P concentration in P-deficient acidic soils.  Soil P-availability affected the ɑ-diversity of bacteria in both bulk and rhizosphere soils.  However, soybean had a stronger effect on the bacterial community composition, as reflected by the similar biomarker bacteria in the rhizosphere soils in both P-treatments.  The relative abundance of biomarker bacteria Proteobacteria was strongly correlated with soil organic-P concentration and AcP activity in low-P treatments.  Further high-throughput sequencing of the phoC gene revealed an obvious shift in Proteobacteria groups between bulk soils and rhizosphere soils, which was emphasized by the higher relative abundances of Cupriavidus and Klebsiella, and lower relative abundance of Xanthomonas in rhizosphere soils.  Among them, Cupriavidus was the dominant phoC bacterial genus, and it was negatively correlated with the soil organic-P concentration.  These findings suggest that soybean growth relies on organic-P mineralization in P-deficient acidic soils, which might be partially achieved by recruiting specific phoC-harboring bacteria, such as Cupriavidus.

Sesame is a labor intensive crop with low mechanized harvest mainly for the seed shattering (SS) trait.  In this study, we performed genetic analysis of seed-shattering resistance (SR) trait with a SR sesame mutant 12M07.  Differing from the SS type, the parenchyma cells in the abscission zone of the 12M07 mutant arrange loosely but adhere to the seed coat. Inheritance analysis of six generations derived from 12M07 (SR)×Xiangcheng Dazibai (SS) showed that SR trait is recessive and controlled by single gene pair.  Association mapping of F₂ population with 888619 variants (SNPs and InDels) and 31884 structural variation (SV) determined that only SV12002 in the 5' upstream region of gene Sindi0765000 (named SiHEC3) in SiChr.3 was significantly associated with SR trait.  SiHEC3 encodes the HLH transcription factor.  A 1049-bp deletion occurred in the 5′ UTR of Sihec3 in 12M07.  SiHEC3 was mainly expressed in developing placental tissues, with the expression peak in 45 days after pollination capsules.  A dual-luciferase reporter assay in tobacco confirmed that the promoter activity of Sihec3 reduced because of the deletion of 1049 bp promoter sequence.  Protein-protein interaction network analysis showed that HEC3 co-expressed with nine key proteins, such as SHATTERPROOF1 (SHP1) and SEEDSTICK (STK) which participate in the secondary wall biosynthesis of the absciss layer in plants.  The findings exhibit the important function of SiHEC3 corresponding with the SR trait and supply the gene information for new variety breeding with high mechanized harvest in sesame and other crops.

As important yield-related traits, thousand-grain weight (TGW), grain number per spike (GNS) and grain weight per spike (GWS) are crucial components of wheat production.  To dissect their underlying genetic basis, a double haploid (DH) population comprised of 198 lines derived from 8762/Keyi 5214 was constructed.  We then used genechip to genotype the DH population and integrated the yield-related traits TGW, GNS and GWS for QTL mapping.  Finally, we obtained a total of 18 942 polymorphic SNP markers and identified 41 crucial QTLs for these traits.  Three stable QTLs for TGW were identified on chromosomes 2D (QTgw-2D.3 and QTgw-2D.4) and 6A (QTgw-6A.1), with additive alleles all from the parent 8762, explaining 4.81–18.67% of the phenotypic variations.  Five stable QTLs for GNS on chromosomes 3D, 5B, 5D and 6A were identified.  QGns-5D.1 was from parent 8762, while the other four QTLs were from parent Keyi 5214, explaining 5.89–7.08% of the GNS phenotypic variations.  In addition, a stable GWS genetic locus QGws-4A.3 was detected from the parent 8762, which explained 6.08–6.14% of the phenotypic variations.  To utilize the identified QTLs, we developed STARP markers for four important QTLs, Tgw2D.3-2, Tgw2D.4-1, Tgw6A.1 and Gns3D.1.  Our results provide important basic resources and references for the identification and cloning of genes related to TGW, GNS and GWS in wheat.

Wheat germplasm is a fundamental resource for basic research, applied studies, and wheat breeding, which can be enriched normally by several paths such as collecting natural lines, accumulating breeding lines, and introducing mutagenesis materials.  Ethyl methane sulfonate (EMS) as an alkylating agent can effectively introduce genetic variations in a wide variety of plant species.  In this study, we created a million-scale EMS population (MEP) that started with the Chinese wheat cultivars ‘Luyan 128’, ‘Jimai 38’, ‘Jimai 44’, and ‘Shannong 30’.  In the M₁ generation, the MEP had huge phenotypical variations, for instance, >3000 chlorophyll-deficient mutants, 2519 compact spikes, and 1692 male sterile spikes; there were also rare mutations, including 30 independent tillers each with double heads.  Some M₁ variations of chlorophyll-deficiency and compact spikes were inheritable, appearing in the M₂ or M₃ generations.  To advance the entire MEP to higher generations, we adopted a single-seed descendent (SSD) approach; all other seed composites of M₂ were used to screen other agronomically important traits, such as for tolerance to the herbicide quizalofop-P-methyl.  The MEP is available for collaborative projects, and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

Flower organ identity in rice is mainly determined by A-, B-, C- and E-class genes, with the majority encoding MADS-box transcription factors.  However, few studies have investigated how the expression of these floral organ identity genes is regulated during flower development.  In this study, we identified a gene named SUPER WOMAN 2 (SPW2), which is necessary for spikelet/floret development in rice by participating in the expression regulation of pistil identity genes such as OsMADS3, OsMADS13, OsMADS58 and DL.  In spw2 mutant, ectopic stigma/ovary-like tissues have been observed in the non-pistil organs, including sterile lemma, lemma, palea, lodicule, and stamen, suggesting that identities of these organs were severely affected by mutations in SPW2. SPW2 encoded a plant-specific EMF1-like protein that involved in the H3K27me3 modification as an important component of the PRC2 complex.  Expression analysis showed that the SPW2 mutation led to the ectopic expression of OsMADS3, OsMADS13, OsMADS58, and DL in non-pistil organs of the spikelet.  The ChIP-qPCR results showed a significant decrease in the levels of H3K27me3 modification on the chromatin of these genes.  Thus, we demonstrated that SPW2 can mediate the process of H3K27me3 modification of pistil-related genes to regulate their expression in non-pistil organs of spikelets in rice.  This study expands our understanding of the molecular mechanism by which SPW2 regulates floral organ identity genes through epigenetic regulation.

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.

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.

Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally. The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference. However, the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear. As the molecular mechanisms of linoleic acid deposition are not well understood, to investigate the main effector genes affecting the linoleic acid content, this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing (RNA-Seq) and weighted gene coexpression network analysis (WGCNA). We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers. Three hundred ninety-nine Tiannong partridge chickens were slaughtered at 126 days of age, fatty acid levels were measured in pectoral muscle, and pectoral muscle tissue was collected for transcriptome sequencing. Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes. KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation. After RNA-Seq-based quality control of 399 pectoral muscle tissues, 13, 310 genes were identified as being expressed. WGCNA was performed, and a total of 26 modules were obtained, eight of which were highly correlated with the linoleic acid content. Four key genes, namely, MDH2, ATP5B, RPL7A and PDGFRA, were screened according to the criteria |GS|>0.2 and |MM|>0.8. The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways. In this study, a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens, and MDH2, ATP5B, RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content. The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle, providing an important reference for the breeding of slow-type yellow-feathered broiler chickens.

Plant-mediated RNA interference (RNAi) has emerged as a promising technology for insect control. The green peach aphid, Myzus persicae, feeds on over 400 species of host plants. Brassica napus (rape) is the second most important oilseed crop worldwide. M. persicae is highly reproductive and causes severe damage to the rape plants due to its quite flexible life cycle. In this study, we tested the RNAi effects of transgenic rape plants on M. persicae. By in-vitro feeding M. persicae with artificial diets containing double-stranded RNAs (dsRNAs) targeting seven aphid genes, we identified a new gene encoding the partitioning-defective protein 6 (Par6) as the most potent RNAi target. Tissue- and stage-expression analysis of Par6 suggested this gene is highly expressed in the embryo and adult stage of M. persicae. We next generated transgenic rape plants expressing dsPar6 by Agrobacterium-mediated transformation and obtained nine independent transgenic lines. Compared to wild-type control plants, transgenic rape lines expressing dsPar6 showed strong resistance to M. persicae. Feeding assays revealed that feeding transgenic rape plants to M. persicae significantly decreased MpPar6 expression and survival rate and impaired fecundity. Furthermore, we showed that the resistance levels to M. persicae are positively correlated with dsPar6 expression levels in transgenic rape plants. Our study demonstrates that transgenic rape plants expressing dsPar6 are efficiently protected from M. persicae. Interfering with the genes involved in embryo development could be the effective RNAi targets for controlling aphids and potentially other insect pests.

Crop improvement is crucial for addressing the global challenges of food security and sustainable agriculture.  Recent advancements in high-throughput phenotyping technologies and artificial intelligence (AI) have revolutionized the field, enabling rapid and accurate assessment of crop traits on a large scale.  The integration of AI and machine learning algorithms with high-throughput phenotyping data has unlocked new opportunities for crop improvement.  AI algorithms can analyze and interpret large datasets, extracting meaningful patterns and correlations between phenotypic traits and genetic factors.  These technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection, reducing the time and cost required for variety development.  However, further research and collaborations are needed to overcome the challenges and fully unlock the power of high-throughput phenotyping and AI in crop improvement.  By leveraging AI algorithms, researchers can efficiently analyze phenotypic data, uncover complex patterns, and establish predictive models that enable precise trait selection and crop breeding.  The aim of this review is to explore the transformative potential of integrating high-throughput phenotyping and AI in crop improvement.  The review will encompass an in-depth analysis of recent advancements and applications, highlighting the numerous benefits and challenges associated with high-throughput phenotyping and intelligence.

Salinity severely affects plant growth and development.  Thus, it is very crucial to identify the genes functioning in salt stress response and unravel the mechanism of plants to against salt stress.  In this study, the phosphoproteomic assay was used.  A total of 123 of the 4000 quantitative analyzed phosphopeptides were obviously induced by salt stress.  The functional annotation of non-redundant protein database (NR) showed that there were 23 differentially expressed transcription factor, including a phosphopeptide covering the Serine 31 in the RAV transcription factor (named SiRAV1). SiRAV1 was located in nucleus.  Phenotypic and physiological analysis showed that overexpressing SiRAV1 in foxtail millet enhanced salt tolerance and alleviated the salt-induced increases of H₂O₂ accumulation, malondialdehyde (MDA) content and percent of electrolyte leakage.  Further study showed that SiRAV1 positively regulated SiCAT expression to modulate the CAT activity by directly binding to the SiCAT promoter in vivo and in vitro.  Moreover, we found that phosphorylation of SiRAV1 at Ser31 site positively regulated salt tolerance in foxtail millet via enhancing its binding ability to SiCAT promoter but not affected its subcellular localization.  Taken together, our results define a mechanism for SiRAV1 function in salt response where salt-triggered phosphorylation of SiRAV1 at Ser31 enhances its binding ability to SiCAT promoter and the increased SiCAT expression contributes to salt tolerance in foxtail millet.

Blast disease caused by the hemibiotrophic ascomycete fungus, Magnaporthe oryzae is a significant threat to sustainable rice production worldwide. Studies have shown that the blast fungus secretes vast arrays of functionally diverse proteins into the host cell for a successful disease progression. However, the final destinations of these effector proteins inside the host cell and their role in advancing fungal pathogenesis remain a mystery. Here, we reported that a putative mitochondrial targeting non-classically secreted protein (MoMtp) positively regulates conidiogenesis and appressorium maturation in M. oryzae. Moreover, MoMTP gene deletion mutant strains triggered a hypersensitive response when inoculated on rice leaves displaying that MoMtp is essential for the virulence of M. oryzae. In addition, cell wall and oxidative stress results indicated that MoMtp is likely involved in the maintenance of the structural integrity of the fungus cell. Our study also demonstrates an upregulation in the expression pattern of the MoMTP gene at all stages of infection, indicating its possible regulatory role in host invasion and the infectious development of M. oryzae. Furthermore, Agrobacterium infiltration and sheath inoculation confirmed that MoMtp-GFP protein is predominantly localized in the host mitochondria of tobacco leaf and rice cells. Taken together, we conclude that MoMtp protein likely promotes the normal conidiation and pathogenesis of M. oryzae and might have a role in disturbing the proper functioning of the host mitochondria during pathogen invasion.

Cotton is one of the most important economic crops in the world and is a major source of fiber in the textile industry.  Strigolactones (SLs) are a class of carotenoid-derived plant hormones involved in many processes of plant growth and development; however, SL functions in fiber development remain largely unknown.  Here, we found that the endogenous SLs were significantly higher in fibers 20 days post-anthesis (DPA).  Exogenous SLs significantly increased fiber length and cell wall thickness.  Furthermore, we cloned three key SL_S biosynthetic genes, namely GhD27, GhMAX3, and GhMAX4, which were highly expressed in fibers, and subcellular localization analyses revealed that GhD27, GhMAX3, and GhMAX4 were localized in the chloroplast.  The exogenous expression of GhD27, GhMAX3, and GhMAX4 complemented the physiological phenotypes of d27, max3, and max4 mutations in Arabidopsis, respectively.  Knockdown of GhD27, GhMAX3, and GhMAX4 in cotton resulted in an increased number of axillary buds and leaves, decreased fiber length, and significantly reduced fiber thickness.  These findings revealed that SLs participate in plant growth, fiber elongation, and secondary cell wall formation in cotton.  These results provide new and effective genetic resources for improving cotton fiber yield and plant architecture.

In this research, green synthesized magnesium oxide nanoparticles (MgO NPs) from lemon fruit extracts and their fungicidal potential was evaluated against Alternaria dauci infection on carrot (Daucus carota L.) under greenhouse conditions.  The scanning and transmission electron microscopy (SEM and TEM) and ultra-violet (UV) visible spectroscopy were used to validate and characterize MgO NPs.  The crystalline nature of MgONPs was determined using selected area electron diffraction (SAED).  MgO NPs triggered substantial antifungal activity against A. dauci when exposed to 50 and 100 mg L^–1 concentrations but the higher antifungal potential was noticed in 100 mg L^–1 under in-vitro conditions.  In fungal inoculated plants, a marked decrease in growth, photosynthetic pigments, and an increase in phenol, proline contents, and defense-related enzymes of carrot were seen over control (distilled water).  However, foliar application of MgO NPs at 50 and 100 mg L^–1 resulted in significant improvement of plant growth, photosynthetic pigments, phenol and proline contents, and defense enzymes activity of carrots with and without A. dauci infection.  Spraying of MgO NPs at 100 mg L^–1 had more plant length (17.11%), shoot dry weight (34.38%), plant fresh weight (20.46%), and root dry weight (49.09%) in carrots when challenged with A. dauci over inoculated control.  The leaf blight indices and percent disease severity were also reduced in A. dauci inoculated plants when sprayed with MgO NPs.  The non-bonding interactions of Alternaria genus protein with nanoparticles were studied using molecular docking.

Integrative cultivation practices (ICPs) are essential in enhancing cereal yield and resource use efficiency.  Although, the ICP effects on the rhizosphere environment of paddy rice and roots remain to be poorly understood.  In this study, four rice varieties were produced in field. The investigation was performed with six cultivation techniques, includes zero nitrogen application (0 N), local farmers' practice (LFP), nitrogen reduction (NR), and three progressive ICP 1–3 comprised of enhanced fertilizer N practice and increased plant density (ICP1), Similar to ICP1 but with alternate wetting and moderate drying instead of continuous flooding (ICP2), in addition to the same practices as ICP2 application of organic fertilizer (ICP3).  ICPs had greater grain production and nitrogen use efficiency. Root length, dry weight, root diameter, activity of root oxidation, root bleeding rate, zeatin and zeatin riboside compositions, and total organic acids in root exudates elevated with the introduction of successive cultivation practices.  ICPs enhanced nitrate nitrogen, activities of urease and invertase, and diversity of microbes (bacteria) in rhizosphere and non-rhizosphere soil, while decreasing ammonium nitrogen content.  The nutrient content (ammonium nitrogen, total nitrogen, total potassium, total phosphorus, nitrate, and available phosphorus) and urease activity in rhizosphere soil were decreased in all treatments in comparison with non-rhizosphere soil, but opposing outcomes were reported for invertase activity and bacterial -diversity.  The main root morphology, physiology and ammonium nitrogen contents in rhizosphere soil at the primary stages were closely correlated with grain yield and internal nitrogen use efficiency.  These findings suggest that the coordinated enhancement of the root system and the environment of rhizosphere under integrative cultivation approaches may participate in a higher rice production.

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.

The construction of food certification system plays a vital role in upgrading export quality, which has been largely overlooked by previous studies. We match industry-level data of Green Food Certification with HS6-digit export data of agri-food products and quantify impact of Green Food Certification on export quality. We identify Green Food Certification as having a significantly positive effect on export quality. The 2SLS estimation based on instrumental variables and a range of robustness checks confirm the validity and robustness of the benchmark conclusions. Further analysis discloses that Green Food Certification improves export quality by raising agricultural production efficiency and brand premiums. Results of heterogeneity analysis show that, by regions, Green Food Certification does more to improve quality among agri-food products exported to developed regions and regions with high levels of import supervision; By products, Green Food Certification has a greater effect on improving export quality among primary products and products vulnerable to Non-Tariff Measures. The above findings could guide agri-food quality certification systems into the future, which in turn could transform and upgrade of agri-food trade.

Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation. The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops. The identification of these hierarchical structures has benefited from the development of experimental approaches, such as 3C-based methods (Hi-C, ChIA-PET, etc.), imaging tools (2D-FISH, 3D-FISH, Cryo-FISH, etc.) and ligation-free methods (GAM, SPRITE, etc.). In recent two decades, numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms, such as regulating enhancer activity and promoter-enhancer interactions. However, there are relatively few studies about the 3D genome in livestock species. Therefore, studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits. In this review, we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies, drawing inspiration to explore the 3D genomics of livestock species. We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Plant height is a key plant architectural trait that affects the seed yield, harvest index and lodging resistance in Brassica napus L., although the genetic mechanisms affecting plant height remain unclear.  Here, a semi-dwarf mutant, df34, was obtained by ethyl methanesulphonate-induced mutagenesis.  Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene, which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing, and this gene was named BnaSD.C3.  Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the “Darmor-bzh” genome, but there was no potential candidate gene for the semi-dwarf trait underlying this interval.  Furthermore, the interval was aligned to the Zhongshuang 11 reference genome.  Finally, combining structural variation analysis, transcriptome sequencing, phytohormone analyses and gene annotation information, BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34.  This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B. napus