Food fraud is an increasingly prevalent deliberate act of deception for profit.  Hence, it is highly necessary to develop robust analytical methods to assess the authenticity of foods.  In recent years, the geographical origin authenticity of fruits has attracted considerable public concern.  The geographical origin of fruit is generally determined based on specific indicators such as elements, stable isotopes, and metabolites.  Many studies have demonstrated that mineral elements and stable isotope ratios are effective indicators for geographical origin authentication as they are directly related to the geographical environment.  Other techniques, such as spectroscopy and chromatography, also exhibit promising potential for fruit origin discrimination and authenticity assessment.  Omics technologies have emerged as a key approach for authenticating the geographical origin of fruit.  The integration of instrumental analysis techniques with machine learning enables high-precision discrimination of fruit geographical origin, and the growing trend toward combining multiple analytical techniques further enhances identification accuracy.  Commonly used methods for geographical origin authentication include linear techniques such as PCA, PLS-DA, and LDA.  Machine learning algorithms, including SVM, RF, and ANN, have also been applied to identify fruit origin with high accuracy.  Future developments in this field should prioritize the consideration of agricultural practices to ensure reliable and practical authentication.  

High-resistant starch rice is a valuable food for human health, especially for individuals with type 2 diabetes, as it supports effective blood sugar control and provides cardiovascular and intestinal benefits.  However, developing rice varieties with high resistant starch content remains a major challenge.  In this study, we identified a mutant, chalk2, with increased chalkiness from the mutant library of indica rice ZJ100.  The chalk2 mutants exhibited significantly higher amylose and protein contents, while total starch and lipid contents were reduced. Analysis of resistant starch in chalk2 revealed substantial increases in two resistant starch (RS) types RS2 and RS3.  Electron microscopy revealed abnormal starch granule development in the endosperm. The chalk2 mutant also showed reduced grain length, width, and thickness, as well as a decreased seed setting rate, which ultimately led to a significant reduction in grain yield.  Through physical localization, Mut-Map analysis, and transgene complementation, we found that SBEIIb was responsible for the chalk2 phynotypes, a member of the starch branching enzyme (SBE) family, specifically expressed in the endosperm.  Furthermore, the expression levels, enzyme activity, and protein abundance of SBEIIb were significantly reduced in chalk2 mutants.  These findings suggest that SBEIIb plays a crucial role in regulating the composition of starch and resistant starch formation in indica rice.

Filament-like plant proteins are intermediate filament proteins that play a major role in the development and growth of plants.  However, no studies have systematically identified or characterized the filament-like plant proteins (FPP) family in plants.  Fifty-nine FPP candidates were found in this study by analyzing the genomes of two dicots and four monocots.  Phylogenetic analysis and multicollinearity mapping showed the relatively conserved evolution of FPP genes in monocots.  In rice, eight OsFPPs were characterized and found to be induced or repressed by abiotic stresses.  Additional genetic evidence showed that OsFPP7-overexpressing rice exhibited increased sensitivity to abscisic acid during the germination stage, disrupted Na⁺/K⁺ homeostasis, and disrupted balance of reactive oxygen species during the seedling stage when exposed to salt stress.  Conversely, the knockout of osfpp7 alleviated abscisic acid (ABA) sensitivity, safeguarded the antioxidant system and sodium ion transport system, and thus enhanced rice salt tolerance.  In the cytoskeleton, the functions of FPPs in controlling salt stress and plant stress tolerance mechanisms are all further elucidated by our findings.

Wheat grain morphology is an important breeding target considering its impact on yield and end-use properties.  However, the genetic basis of grain roundness, a major determinant of grain morphology, remains largely unexplored.  In this study, an F₂ and a recombinant inbred line (RIL) populations from Zhongkemai 138 (ZKM138)×Chinese Spring (CS) cross were employed to analyze the genetic basis of grain shape variation.  Kompetitive Allele Specific PCR (KASP) markers were developed according to single nucleotide polymorphism (SNP) from bulked segregant exome sequencing (BSE-Seq) of F₂ and Wheat 55K SNP array data online, and then were used to construct two genetic maps of F₂ and RIL populations, spanning 148.89 cM (30 KASP markers) and 129.82 cM (25 KASP markers), respectively.  By the traditional QTL mapping method based on these two maps, a stable quantitative trait locus (QTL) for grain roundness (GR), QGr.cib-5A, could be repeatedly highlighted in the interval of 444.8-455.5 Mb on chromosome 5A.  Further conditional QTL mapping analysis revealed that grain width was the major contributor to GR at this locus.  Besides, the utilization of two tightly linked markers 5A4-15 and 55k-31 showed a 96.27% transmissibility of ZKM138-derived alleles in 134 ZKM138 derivatives alongside a 7.38% increase in GR, and a 65.19% distribution of worldwide varieties.  Finally, TraesCS5A02G236400, possibly encoding a hydroxyproline-rich glycoprotein family protein, was deduced to be the candidate gene.  Collectively, these results provided the possibility of facilitating wheat grain shape improvement and enhancing wheat market value.

Rapeseed (Brassica napus L.) is a major oil crop worldwide that is vigorously promoted for cultivation in China.  Boron (B) is an essential micronutrient for plant growth and development.  However, the agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency.  Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed, yet the genetic basis for variations in B efficiency-related traits remains unclear.  In this study, a natural population with 391 rapeseed accessions and a nutrient solution system were used to investigate B efficiency-related traits, including relative root length (RRL), shoot dry weight (SDW), root dry weight (RDW), and B efficiency coefficient (BEC), all of which exhibited extensive phenotypic variations under B deficiency.  Through a genome-wide association study (GWAS) of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing, 106 significantly associated SNPs were identified by employing both the general linear model and the mixed linear model.  Among these SNP loci, two prominent SNP clusters were detected on chrA03: 14,087,835–14,764,672 and chrC03: 20,110,319–22,135,492 at low B levels across three repeated experiments of multiple traits.  Integrating those results with a transcriptome analysis, four genes exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region, BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D, were identified as candidate genes that could potentially be involved in efficient B utilization, and their favorable haplotypes were found to improve seedling growth and productivity under B deficiency.  Considering the lack of B mineral resources in China, the rapid and accurate identification of more B-efficient alleles and studying the genetic mechanism underlying crop responses to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green, sustainable agriculture.

Chloroplast gene expression relies on nucleus-encoded factors for RNA metabolism processing, but the mechanisms under cold stress remain poorly understood.  In this study, we isolated and characterized a foxtail millet (Setaria italica) mutant, temperature-sensitive chlorophyll-deficient (sitcd1), which exhibited reduced chlorophyll content and abnormal chloroplasts, resulting in an albino phenotype during early leaf development at low temperatures (20°C during the day and 18°C at night).  Map-based cloning revealed that SiTCD1 encoded a P-type PPR protein localized in chloroplasts.  In sitcd1 background, transgenic lines of SiTCD1 overexpression appeared nearly normal green leaves under L20/D18 condition.  SiTCD1 was especially expressed in earlier development of leaves under low temperature.  Additionally, SiTCD1 directly bound to the plastid gene atpF in vitro, which might participate in the splicing of plastid gene atpF under low temperature.  RNA-seq indicated that the expression of genes related to metabolism (such as porphyrin, chlorophyll and glutathione metabolism), which required ATP for energy, was down-regulated in sitcd1, resulting in decreased chlorophyll content, GSH, and its redox couple (GSH/GSSG) at low temperature.  As sitcd1 exhibited more sensitive at the bud bursting stage than germination and seedling stage under cold stress, we identified two haplotypes of SiTCD1 (SiTCD1^Hap1 and SiTCD1^Hap2) in 195 accessions, and found that accessions carrying the SiTCD1^Hap2 allele were more tolerant to cold stress than those with the SiTCD1^Hap1 allele at the bud bursting stage.  In summary, our results suggest that SiTCD1 is essential for early chloroplast development under low temperature in foxtail millet.

Globally recurrent extreme high temperature (HT) events severely limit rice production.  This study investigated whether a controlled moderate soil drying (MD) could replace the conventional well-watered (WW) regime to more effectively mitigate HT stress on pistil fertilization in photo-thermosensitive genetic male-sterile (PTGMS) rice, and examined the role of brassinosteroids (BRs).  Two PTGMS rice varieties were cultivated under normal temperature (NT) and HT conditions, paired with WW and MD strategies during anthesis.  In the conventional WW regime, waterlogging reduced BR levels in roots and pistils due to excessive decomposition, weakening active water uptake driven by root activity and failing to alleviate transpiration-pulled passive water extraction hampered by restricted stomatal openings.  Thereby, it caused water imbalance in plants and weakened pistil function due to a suppressed ascorbate-glutathione (AsA-GSH) cycle and hyperactive nicotinamide adenine dinucleotide phosphate oxidase (NOX) activity.  This exacerbated pistil fertilization impairment and hybrid seed yield loss under HT stress.  Conversely, by promoting BR synthesis and inhibiting its decomposition in roots and pistils, the MD strategy enhanced root activity and transpiration-driven water uptake.  It maintained plant water balance and supported pistil function by suppressing NOX activity and enhancing AsA-GSH cycle-driven redox homeostasis.  Thus, it mitigated HT-induced pistil fertilization impairment and hybrid seed yield loss.  The precise function of BRs in moderating the protective effects of MD against the detrimental impacts of HT stress on pistil fertilization in PTGMS rice was confirmed through genetic and chemical approaches.  Consequently, a controlled MD method proved more effective than the conventional WW regime in alleviating HT stress on pistil fertilization in PTGMS rice by promoting BR enhancement.

Single-time fertilization (STF) with controlled release blended fertilizer (CRBF) improves grain yield and nitrogen use efficiency (NUE) in rice production.  However, the impact of soil nitrogen (N) distribution and root growth on rice yield and NUE under STF with CRBF remains unclear.  Here, a two-year field experiment investigated the effects of two fertilizer types (normal urea (U) and CRBF) and two single-time fertilization methods (broadcast and side-deep fertilization) on the soil N distribution, plant N uptake, root characteristics, grain yield, and NUE.  The results showed that CRBF under STF increased the averages of plant dry matter accumulation, N uptake, grain yield, nitrogen recovery efficiency (NRE), and nitrogen agronomic efficiency (NAE) by 8.29, 21.85, 10.57, 79.28, and 74.8% compared to the other treatments, respectively.  Side-deep fertilization with CRBF further increased NUE by 12.78% compared to broadcast.  Moreover, CRBF under STF increased the leaf SPAD value and glutamine synthetase (GS)/glutamine oxoglutarate aminotransferase (GOGAT) activity by 5.93 and 25.58%, respectively.  CRBF under STF increased the soil inorganic N concentration and showed a “rising early and stabilizing later” pattern.  In addition, CRBF under STF improved rice root growth and increased the averages of root biomass, total root number, root average diameter, total root length, total root surface area, and total root volume by 28.30, 28.56, 18.64, 13.38, 35.26, and 37.06%, respectively, at the tillering and heading stages.  Partial least squares path modeling indicated that CRBF under STF increased the soil inorganic N concentration which improved root morphology, thereby increasing N uptake and improving the rice yield and NUE.  Taken together, our findings show that CRBF with single-time fertilization is the preferred N fertilizer strategy for achieving high yield and efficiency in rice, and that side-deep fertilization is the optimal fertilization method.

The application of slow-controlled release fertilizer is a simple and labor-saving cultivation technology that can improve the yield and nitrogen use efficiency (NUE) of wheat, although research on the impact of a single application of controlled-release nitrogen (N) fertilizers with different release periods on wheat grain quality is still limited.  In this study, urease inhibitor urea (AHA), sulfur-coated urea (SCU), a combination of SCU and AHA fertilizer (BSAF) and blended slow-controlled release fertilizer (BRNF) were used to investigate the effect of slow-controlled release fertilizers on the nutrient release, grain yield, NUE, and protein content of soft wheat.  The goal was to determine the effect of a one-time application of controlled release fertilizer on wheat grain yield and protein content and its underlying mechanisms.  The results showed that the different slow-controlled release fertilizer treatments had significantly different N release rates.  AHA presented a fast release mode, while SCU and BSAF presented slow-release modes, and BRNF presented a controlled release mode.  Compared with CK, BRNF increased grain yield and reduced the protein content of soft wheat, with an average increase of 6.73% in grain yield and a reduction of 1.85% in protein content.  The higher N absorption of BRNF led to greater NUE, N agronomic efficiency (NAE) and N apparent recovery fraction (NRF).  However, AHA, SCU and BSAF all showed the opposite trend.  Compared with CK, BRNF improved post-anthesis dry matter accumulation (PDMA) and the contribution rate of dry matter accumulated post-anthesis to the grain (CDA), while reducing post-anthesis N accumulation (PNA) and the contribution rate of post-anthesis N accumulation to grain (CNA).  The main reasons for the improvement in yield and reduction in protein content were related to the increases in PDMA and CDA, and the reductions in PNA and CNA, respectively.  Therefore, BRNF is an effective agronomic strategy for promoting the coordination of grain yield and quality in soft wheat.

The effects of maize straw return and N fertilizer application on soil quality and crop yield have been extensively investigated.  However, the effects of different amounts of maize straw returned to the field with different nitrogen application rates on the soil–crop system quality, abundance of functional N cycle microorganisms, N₂O emissions, and crop N nutrition status of crops have not been thoroughly explored.  The objective of this study was to assess the effects of different summer maize straw return rates and N application rates on i) soil quality and crop productivity; ii) the community of N cycle functional microorganisms and N₂O emission; and iii) crop N status.  The results indicated that crop yields increased by 7.62 to 12.69% at 210 kg ha^–1 of N application for full straw return (SN) and half return (1/2SN) compared to the no-return treatment (CK).  No significant difference was noted in the yields between the full straw return reduced by 15% (178.5 kg N ha^–1) of N fertilizer (S-15%N) and SN.  The surface soil layer (0–20 cm) showed significantly higher levels of soil organic matter (SOM), the community of N-cycling functional microorganisms, crop N nutrition status and N uptake efficiency in SN, 1/2SN, and S-15%N as compared to other treatments.  Compared to SN, S-15%N and 1/2SN reduced cumulative N₂O emission fluxes by 19.11 and 5.51%, respectively.  Furthermore, the nitrogen nutrient index (NNI) values of 1/2SN and S-15%N were closer to the critical N requirement than SN.  In summary, schemes for determining the optimal rates of straw return and N application (1/2SN and S-15%N) based on SOM, NNI, cumulative N₂O emission fluxes, and yield can be applied to the annual production of winter wheat and summer maize in China.