BACKGROUND:Antibiotic fermentation residues, which contain antibiotic remnants and other potentially hazardous components, present increasing risks when illegally incorporated into animal feed. Their addition can promote the spread of antimicrobial resistance, drug accumulation, and ultimately threaten food safety and public health. Although regulatory control is required, existing analytical methods suffer from poor specificity, low accuracy, and limited applicability in practical settings. Therefore, there remains an urgent need for a rapid, accurate, and practical detection method to identify antibiotic fermentation residues directly within diverse feed matrices. RESULTS:We established three real-time PCR detection systems by designing primer-probe sets targeting OxyA, NeoN and AveD, the core biosynthetic genes of oxytetracycline-, neomycin- and avermectin-producing strains. The assay workflow is streamlined and requires only simple DNA extraction, without the need for chemical cleanup or feed matrix pretreatment. All reactions were completed within 2 h, demonstrating high operational efficiency suitable for routine monitoring. Sensitivity evaluation showed that fermentation residues could be reliably detected at a minimum level of 1% (w/w) in feed, and no cross-amplification occurred with non-target antibiotic residues or diverse feed ingredients. Artificially adulterated samples verified robust applicability across matrices including soybean meal, cottonseed meal and compound feed additives. Repeatability assessment further confirmed excellent stability, with intra- and inter-assay CV values maintained below 2%. These results collectively demonstrate that the developed assays are rapid, accurate and highly adaptable to real feed-testing environments. SIGNIFICANCE:This work represents the first demonstration of real-time PCR detection of multiple antibiotic fermentation residues in feed based on strain-origin specific biosynthetic genes. The method provides a rapid, sensitive, accurate, and high-specificity molecular tool for on-site regulatory screening, enabling early identification of the illicit addition of antibiotic fermentation residues. The application of this technology strengthens feed safety surveillance and contributes to preventing antibiotic-related hazards and safeguarding public health.

INTRODUCTION:Achieving both high yield and superior grain quality remains a major challenge in rice breeding due to the long-standing trade-off between these traits. Enhancing vascular transport efficiency may provide a strategy to overcome this constraint, yet the genetic basis linking peduncle vascular architecture with yield-quality coordination remains poorly understood. OBJECTIVE:This study aimed to develop a flow-centered molecular design framework targeting vascular transport capacity to reconcile yield and quality in Oryza sativa. METHODS:Using 248 accessions from the 3 K Rice Genomes panel, 14 traits related to peduncle vascular bundles, yield, and quality were phenotyped, and 31 cloned genes were haplotyped. Haplotype validity was confirmed by functional verification using near-isogenic or transgenic lines. Trait correlations, genetic effects, and pyramiding interactions of key genes were assessed. Superior haplotypes were converted into KASP markers and tested across 221 released cultivars. A breeding strategy was proposed and validated using introgression lines. RESULTS:The peduncle vascular bundles play a crucial role in simultaneously enhancing single-panicle weight and grain appearance quality in japonica/geng rice. Five key genes (GL3.1, GW5, FLO2, LVPA4, and RST1) were identified as synergistic regulators enhancing vascular development, panicle weight, and grain quality without compromising yield. A pyramiding-effect network of genes to guide the simultaneous improvement of yield and quality were constructed. Based on the uneven distribution of superior alleles among modern cultivars, a flow-centered molecular design breeding strategy was subsequently proposed and validated through the development of introgression lines, confirming that optimizing vascular systems can simultaneously improve yield and quality. CONCLUSIONS:This study establishes a flow-centered genetic and conceptual framework linking vascular bundle architecture to yield-quality coordination and provides practical molecular tools for next-generation high-yield, high-quality rice breeding, while also offering a strategic reference for similar improvements in other crops such as wheat and maize.

Drought stress is a major limitation to global wheat production. Here, we demonstrate that the wheat gene TaCOMT1A, encoding a caffeic acid O-methyltransferase, plays a crucial role in enhancing drought tolerance in wheat. Overexpression of TaCOMT1A significantly improved drought tolerance at the seedling stage, as evidenced by higher survival rates, biomass, and antioxidant capacity, along with reduced oxidative damage in transgenic lines. Field trials demonstrated that these lines maintained superior grain yield under limited irrigation. We identified TaCOMT1A as a multifunctional enzyme capable of synthesising both the flavonoid sakuranetin and melatonin in vitro. Metabolomic and functional analyses confirmed that sakuranetin is a key downstream metabolite mediating the drought tolerance conferred by TaCOMT1A. Exogenous application of sakuranetin enhanced drought tolerance across diverse wheat cultivars and, importantly, rescued the susceptible phenotype of TaCOMT1A EMS mutants (E829 and E830). Mechanistically, sakuranetin treatment bolstered the antioxidant system and attenuated oxidative stress under drought. Furthermore, both TaCOMT1A overexpression and sakuranetin application reduced plant height by suppressing gibberellic acid (GA3) biosynthesis. Crucially, field application of sakuranetin increased grain yield under both well-irrigated and drought conditions. Our results establish a novel pathway where TaCOMT1A enhances drought tolerance and modulates plant architecture primarily through the production of sakuranetin, positioning this metabolite as a promising plant-based priming agent for sustainable wheat cultivation.

Rice stands as one of the world’s most essential cereal crops, underpinning global food security and economic stability. Salinity-alkalinity stress represents a major environmental constraint that severely impairs rice growth, with mesocotyl elongation being particularly vulnerable. Despite its agronomic importance, the genetic basis of mesocotyl tolerance to combined saline-alkaline stress remains largely unexplored. In this study, we measured mesocotyl length (ML) and relative ML traits under salt-alkali stress and control conditions in a 148-line doubled haploid (DH) population constructed from Sea Rice 86 and Nipponbare (Nip) plants. By constructing a high-density genetic map, we identified two loci significantly associated with mesocotyl elongation under stress, one governing salt tolerance and the other conferring alkali tolerance. Through integrative gene functional annotation and haplotype analysis, we identified two key candidate genes (LOC_Os03g49260 and LOC_Os03g49500) regulating ML, three genes (LOC_Os04g52479, LOC_Os04g52510, and LOC_Os04g52725) linked to salt tolerance, and one pivotal gene (LOC_Os03g01410) associated with alkali tolerance. An effective strategy for enhancing rice ML under salt-alkali stress could be the pyramiding of favorable haplotypes from multiple candidate genes to achieve an optimal haplotype combination. These findings not only provide critical insights into the genetic mechanisms of salinity‒alkalinity tolerance in rice but also provides a functional roadmap for developing resilient rice varieties equipped with superior mesocotyl traits and improved stress adaptability.

This study established an optimized CTAB-based DNA extraction method for edible oils, which enables stable and reliable DNA recovery from commercially available edible oils for authenticity identification and adulteration detection. Real-time PCR was used to assess DNA precipitation time and organic solvent extraction, revealing that longer precipitation increased inhibitors, hindering PCR amplification, while organic solvents enhanced efficiency. The method was applied to detect adulteration in commercially available soybean and olive oils. A standard curve based on real-time PCR Ct values demonstrated the ability to detect as low as 10% soybean oil in olive oil, with recovery rates of 92% and 80% for samples spiked with 70% and 30% soybean oil, respectively. The coefficients of variation (CV) were 11% and 14%, within acceptable ranges. This reliable method provides a valuable tool for edible oil authentication and adulteration detection.

Rice (Oryza sativa L.), a staple food for more than half of the global population, is moderately salt-sensitive and increasingly threatened by soil salinization. Deciphering the genetic mechanisms of salt tolerance (ST) is pivotal for accelerating genetic improvement of ST by rice molecular breeding and safeguarding global food security. A quantitative trait locus for rice ST, qRLS8, was mapped using a BC2F7 backcross introgression line population derived from the cross between Minghui 63 and 02428. Combined with transcriptome analysis, Lhca4, encoding a subunit of the light-harvesting complex, was identified as the candidate gene of qRLS8. Lhca4 positively regulates rice ST at seedling stage based on the phenotypic verification using knockout and overexpression transgenic lines of Lhca4. Overexpression of Lhca4 increased the activities of superoxide dismutase and peroxidase, and decreased the accumulation of H2O2 and O2−, holding a high photochemical efficiency under salt stress conditions. In contrast, knockout of Lhca4 increased accumulation of reactive oxygen species (ROS) in rice, resulting in disruption of the chloroplast lamellae and a decrease in photosynthetic efficiency. Transcriptome analysis revealed that Lhca4 mediated salt stress response pathway involved in metabolic regulation, enzyme activity regulation, and antioxidant regulation. Lhca4 confers rice ST by preserving chloroplast integrity, maintaining photochemical efficiency, and systemically modulating ROS homeostasis through enhancing antioxidant defense system. These findings provide a valuable gene target for the development of salt-tolerant rice varieties without compromising photosynthetic capacity.

Pentatricopeptide repeat (PPR) proteins are key regulators of organelle RNA metabolism in plants, yet their precise mechanisms in chloroplast RNA processing remain unclear. Here, we identify WPR, a unique P-type PPR protein in rice (Oryza sativa L.), as a critical factor in chloroplast RNA splicing and editing. A ~112-kb chromosomal inversion upstream of WPR causes an albino panicle rachis phenotype (wpr mutant), while complete loss of WPR function leads to seedling lethality. WPR deficiency disrupts the splicing of multiple group II introns (atpF, ndhA, ndhB, petB, rpl2, and rps12) and impairs RNA editing in transcripts such as ndhA, ndhB, ndhG, rps14, and ycf3. Electrophoretic mobility shift assay (EMSA) data confirm that WPR directly binds to precursor mRNAs of atpF, ndhA, petB, rpl2, and rps12. Strikingly, WPR interacts with both RNA editing factors (MORF1, MORF8b) and the splicing factor CAF2, but not with other PPR proteins targeting the same transcripts. Unlike most PPR proteins, WPR contains only six PPR repeats, which is the fewest among all functionally characterized rice PPR proteins. With few informative repeats, WPR likely possesses a broad, low-specificity RNA-binding activity. Moreover, WPR may act on chloroplast RNA maturation by recruiting MORFs and CAF2 rather than other PPR proteins, highlighting a novel regulatory mode in which P-type PPR protein may act as an RNA-binding scaffold to integrate diverse RNA-processing machineries. This study advances the understanding of PPR protein diversity and provides new insights into the molecular mechanisms of chloroplast RNA processing in rice.

Nitrogen is a crucial element that impacts rice yield and its constituent factors. The effects of reduced nitrogen levels on yield constitute is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 562 MAGIC line population and 284 germplasm varieties were used for genome-wide association analysis (GWAS) and haplotype analysis, aiming to detect quantitative trait loci (QTL) and candidate genes associated with tolerance to low nitrogen levels. The ratio of effective panicle number per plant (REPN), total number of grains per panicle (RTGN), seed setting rate (RSSR), thousand grain weight (RTGW), biomass (RBM), harvest index (RHI), and grain yield per plant (RGY) of low to normal nitrogen conditions were measured in this study. The RBM and RHI were directly closely related to RGY, while the RSSR indirectly and positively affected RGY through RHI, and the REPN and RTGN mainly indirectly and positively affected RGY through RBM. LOC_Os06g06440 was the most likely gene affecting low-nitrogen-tolerance-related traits in rice within the region, ranging from 2.898 Mb to 3.046 Mb (148 kb) on chromosome 6, and the haplotype AA, with a significantly larger mean RGY of 0.95 and 1.53 in the MAGIC and germplasm varieties, respectively, was the advanced allele of LOC_Os06g06440. Nine xian (indica) varieties (IRIS_313-11624, IRIS_313-10932, CX382, B067, B249, IRIS_313-8215, IRIS_313-10544, B052, and B233) carrying the superior haplotype (AA) of LOC_Os06g06440 and having a higher RGY were selected for the molecular marker-assisted selection of low nitrogen tolerance in rice. These results will enhance our knowledge of the genetic basis of tolerance to low levels of nitrogen and provide valuable information for improving tolerance to low levels of nitrogen in rice-breeding programs.

BACKGROUND:Rice, being a thermophilic crop, exhibits high sensitivity to low-temperature stress throughout its growth and development. Consequently, enhancing cold tolerance (CT) has been a paramount objective in rice breeding programs. The budding and seedling stages are particularly susceptible to low-temperature damage, making it crucial to improve CT during these stages to ensure the stable establishment and development of the rice population. RESULTS:In this study, we exposed the parental lines Nipponbare (NIP) and Searice 86 (SR86), along with their derived 170 doubled-haploid (DH) population lines, to cold treatments during both the budding and seedling stages. Quantitative trait locus (QTL) mapping was performed using statistical indices such as the survival rate at the budding stage (SRBS), severity of damage at the budding stage (SDBS), survival rate at the seedling stage (SRSS), and wilting degree at the seedling stage (WDSS). This analysis identified four QTLs at the budding stage and eight QTLs at the seedling stage. Furthermore, by integrating differentially expressed genes (DEGs) from transcriptomic data with genes located within the QTL regions, we identified 10 candidate genes for the budding stage and 11 candidate genes for the seedling stage. Based on DNA sequence variations between the parental lines, changes in gene expression under cold treatment, and haplotype analyses, the key candidate genes were ultimately determined to be Os02g0250600 for the budding stage and Os06g0696600 for the seedling stage. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of transcriptomic data from both stages revealed significant differences in the regulatory pathways involved in CT between the budding and seedling stages. CONCLUSION:The results indicate that Os02g0250600 is the pivotal gene responsible for CT at the budding stage, with haplotype 4 exhibiting the highest level of CT. Meanwhile, Os06g0696600 plays a crucial role in CT at the seedling stage, where haplotypes 2 and 4 have been identified as advantageous. A comprehensive analysis integrating QTL and transcriptome data from both stages revealed distinct differences in CT mechanisms, highlighting stage-specific variations. This study provides valuable theoretical insights and practical references for the cloning of CT genes and the development of cold-tolerant rice varieties during the budding and seedling stages.

Molecular property prediction is essential in diversified applications, as it helps identify molecules with the desired characteristics. However, the task often suffers from limited data, making the few-shot learning challenging. We introduce a Context-informed Few-shot Molecular Property Prediction via a Heterogeneous Meta-Learning approach, which employs graph neural networks combined with self-attention encoders to effectively extract and integrate both property-specific and property-shared molecular features, respectively. Based on the property-shared molecular features, we further infer molecular relations by using an adaptive relational learning module. The final molecular embedding is improved by aligning with the property label in the property-specific classifier. Furthermore, we employ a heterogeneous meta-learning strategy that updates parameters of the property-specific features within individual tasks in the inner loop and jointly updates all parameters in the outer loop. This enhances the model's ability to effectively capture both general and contextual information, leading to a substantial improvement in predictive accuracy. The model's performance was rigorously evaluated across various real molecular datasets, showcasing its superiority over current methods, especially in challenging few-shot learning scenarios.

AtbZIP69 overexpression in wheat significantly enhanced drought and low nitrogen tolerance by modulating ABA synthesis, antioxidant activity, nitrogen allocation, and transporter gene expression, boosting yield. In this study, we generated wheat plants with improved low nitrogen (LN) and drought tolerance by introducing AtbZIP69, a gene encoding a basic leucine zipper domain transcription factor, into the wheat cultivar Shi 4056. AtbZIP69 localized to the nucleus and activated transcription. A greenhouse study further revealed that, compared to wild type (WT) wheat, AtbZIP69 transgenic wheat exhibited significantly increased drought and LN stress tolerance. Under drought stress, the H2O2 concentration in transgenic lines decreased, whereas SOD activity and proline content increased, resulting in remarkably enhanced drought resistance. Furthermore, drought stress boosted the expression of critical abscisic acid (ABA) synthesis enzymes as well as the ABA content of transgenic plants, implying that this gene may improve wheat’s drought resistance by promoting ABA production. Additionally, during a two-year field test, the yield and the number of spikes of transgenic wheat were significantly higher than those of WT wheat under LN conditions. Mechanistically, the overexpression of AtbZIP69 altered nitrogen distribution by allocating more nitrogen to grains under LN conditions. In addition, the expression of genes encoding nitrogen transporter proteins was higher in AtbZIP69 transgenic wheat than in WT wheat under LN conditions. These findings suggest that the insertion of AtbZIP69 opens up new opportunities for wheat stress resistance breeding.

Drought stress is one of the main abiotic stressors affecting wheat yield. In recent years, plant-derived compounds have played a key role in improving wheat stress resistance and have been widely used to enhance crop drought resistance and yield. Currently, flavonoids, as important secondary metabolites in plants, are related to drought resistance. In this study, we found through screening that the flavonoid compound dihydroquercetin can improve the drought resistance of wheat. The results indicate that exogenous dihydroquercetin can significantly improve the survival rate, relative water content, fresh weight, and dry weight of wheat seedlings under drought conditions. Biochemical assays combined with transcriptome analysis demonstrate that under drought stress, dihydroquercetin simultaneously enhances antioxidant capacity and upregulates the expression of β-glucosidase (BGLU2) and aldehyde dehydrogenase (ALDH) in the phenylpropanoid biosynthesis pathway. These changes collectively enhance the antioxidant capacity of wheat and reduce the content of superoxide anions and hydrogen peroxide. Dihydroquercetin also upregulated the expression of important genes in the glycerophospholipid metabolism pathway, including phospholipase D (PLD), no special phospholipase C (NPC), and glycerophosphodiesterase (GDPD), alleviating damage to the cell membrane, reducing malondialdehyde content. Therefore, the application of dihydroquercetin improves drought resistance in wheat by promoting antioxidant capacity and alleviating drought-induced oxidative damage. This study lays the groundwork for implementing dihydroquercetin to boost wheat's drought resilience in agricultural settings.

Alkaline soil is characterized by high soluble salt content, elevated pH levels, and ionic imbalance, all of which collectively intensify the harmful effects of alkaline stress on plants. To gain molecular insights into alkaline tolerance (AT), we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage. A total of 2 929 764, 2 059 114, and 1 365 868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies (GWAS) in the entire population as well as in the xian and geng subpopulations, respectively. Candidate genes and their superior haplotypes were further identified through gene-based association, haplotype analysis, and gene function annotation. In total, 99 QTLs were identified for AT by GWAS, and three genes (LOC_Os03g49050 for qSSD3.1, LOC_Os05g48760 for qSKC5, and LOC_Os12g01922 for qSNC12) were selected as the most promising candidate genes. Furthermore, we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits. This study identified crucial candidate genes and their favorable alleles for AT traits, laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.

Soil alkalization is one of the most severe abiotic stresses constraining rice yields. However, the genetic basis underlying alkaline tolerance of rice remains poorly understood. Here, we used genome-wide association analysis to identify OsNPF7.3 as the candidate gene for qAT4 , which is a major locus associated with alkaline tolerance at rice seedling stage. OsNPF7.3 encodes a nitrate/oligopeptide transporter and acts as a negative regulator of rice alkaline tolerance. A natural variation of 7-bp insertion/deletion in the OsNPF7.3 promoter, affecting the binding affinity of transcription factor OsDOF11, mainly contributes to differential transcriptional levels of OsNPF7.3 , and thus leads to differential alkaline tolerance between japonica and indica subspecies. OsNPF7.3 localizes to the vacuolar membrane and mediates nitrogen transport from older to younger leaves under alkaline stress. Loss of OsNPF7.3 significantly upregulated the expression of nitrogen metabolism-related genes and metabolites, suggesting its regulatory role in nitrogen allocation. Together, these findings reveal an OsDOF11- OsNPF7.3 -nitrogen metabolism regulatory module that connects nitrogen homeostasis to alkaline tolerance, providing a promising target for the development of alkaline-tolerant rice varieties.

Salinity is one of the main environmental factors influencing rice production. Many genes affecting salt tolerance (ST) have been cloned in rice so far. In the present study, four genes negatively regulating ST, including HST1, LRRK1, STRK2, and PC1, were edited by CRISPR-Cas9 technology in six rice varieties (three in indica (xian) and three in japonica (geng) backgrounds), and three two-gene editing combinations, including hst1-lrrk1, hst1-strk2, and hst1-pc1, were created. All combinations of hst1-pc1, hst1-lrrk1, and hst1-strk2 significantly improved the ST of all the tested materials in both xian and geng backgrounds and had much better ST than single-gene editing lines. The combination of hst1-pc1 had the poorest ST in CH70 and 8TX23 backgrounds but showed almost the same level of ST as the combinations of hst1-strk2 and hst1-lrrk1 in the C199S background for 17 days after salinization, which clearly brought out the background effect on ST and its utilization in ST breeding. As a comparison of the recipient varieties, almost all gene-edited lines except hst1-pc1 in the CH70 background showed significantly reduced grain weight owing to reduced seed setting rate in normal conditions. The hst1-strk2 showed the highest level of ST at the seedling stage and a relatively higher grain yield among all the lines; thus, it is feasible to enhance the ST of high-yielding rice varieties by simultaneously gene-editing against the two loci or pyramiding these two alleles with the other major ST genes of rice. Our results provide valuable gene resources and germplasms for improving rice salt tolerance and high yield.

Drought stress constitutes a significant challenge for plant growth, particularly impacting sugarcane yield and quality. MYB transcription factors play a pivotal role in regulating drought tolerance in plants, yet investigations into the 3R-MYB subfamily remain limited. Here, we identified 35 sugarcane 3R-MYB genes, in which ScMYB3R1 significantly responds to PEG and ABA treatments. The overexpression of ScMYB3R1 enhanced drought tolerance in Arabidopsis through reducing water loss and activating ABA signaling. Through global gene expression profiling, we found that numerous differentially expressed genes were enriched in ABA signaling and drought stress response pathways. Notably, ScMYB3R1 regulated 28.8% of ABA-induced genes and 29.9% of ABA-repressed genes. Further analysis revealed that ScMYB3R1 physically interacts with the ABA receptor ScPYL61, and they collaboratively activate ABA signaling. Additionally, ScPYL61 interacts with the type 2C protein phosphatase ScPP2C57, and ScMYB3R1 promotes this interaction. These findings collectively reveal a novel molecular module, ScMYB3R1-ScPYL61-ScPP2C57, in sugarcane that contributes to drought tolerance in an ABA-dependent manner. This research not only identifies potential candidate genes for improving drought tolerance in sugarcane but also expands our understanding of the functional roles of the 3R-MYB subfamily and ABA signaling mechanisms.

Aromatic rice has gained significant attention due to its high economic and nutritional value. 2-Acetyl-1-pyrroline (2-AP), a key aroma compound in aromatic rice, plays a crucial role in elucidating the aroma characteristics of aromatic rice. However, there is no report on the effect of aromatic rice in rice–potato rotation on aroma characteristics. In order to study the influences of winter-planted potatoes on the yield, quality, and 2-AP biosynthesis of aromatic rice grains, the commonly cultivated aromatic rice variety Meixiangzhan-2 and the potato cultivar Huashu-5 were selected as experimental materials for a three-year consecutive field experiment with different tillage patterns consisting of rice–winter fallow as the control group (CK) and rice–potato rotation as the experimental group (RP). The results indicated that the RP treatment enhanced the soil nutrient content and decreased the bulk density. Compared with CK, RP treatment increased the effective panicle number by 10.88% and grain number per panicle by 8.82%, thereby increasing the yield by 11.99%. Meanwhile, RP treatment improved the brown rice rate by 2.61%, milled rice rate by 4.53%, head milled rice rate by 7.51%, and crude protein content by 6.98%. Regarding 2-AP biosynthesis in grains, in contrast to CK, the RP treatment raised the levels of related precursors (Δ1-pyrroline, Δ1-pyrrolidine-5-carboxylic acid, and proline increased by 8.95%, 18.14%, and 13.75%, respectively) and enzymes (proline dehydrogenase, ornithine transaminase, and diamine oxidase increased by 18.37%, 14.61%, and 11.36%, respectively) in its synthesis pathway, thereby facilitating the accumulation of 2-AP. Furthermore, we also observed a more stable yield and grain 2-AP content in aromatic rice under RP treatment. Overall, with regard to enhancing the aromatic rice yield and aroma, the rice–potato rotation system can be contemplated for vigorous promotion.

Soybean (Glycine max [L.] Merr.) is a valuable oil crop but is also highly susceptible to environmental stress. Thus, developing approaches to enhance soybean stress resistance is vital to soybean yield improvement. In previous studies, transcription factor Alfin has been shown to serve as an epigenetic regulator of plant growth and development. However, no studies on Alfin have yet been reported in soybean. In this study, the endoplasmic reticulum (ER) stress- and reactive oxygen species (ROS)-related GmAlfin09 was identified. Screening of genes co-expressed with GmAlfin09 unexpectedly led to the identification of soybean peroxidase 6 (GmPRDX6). Further analyses revealed that both GmAlfin09 and GmPRDX6 were responsive to ER stress, with GmPRDX6 localizing to the ER under stress. Promoter binding experiments confirmed the ability of GmAlfin09 to bind to the GmPRDX6 promoter directly. When GmAlfin09 and GmPRDX6 were overexpressed in soybean, enhanced ER stress resistance and decreased ROS levels were observed. Together, these findings suggest that GmAlfin09 promotes the upregulation of GmPRDX6, and GmPRDX6 subsequently localizes to the ER, reduces ROS levels, promotes ER homeostasis, and ensures the normal growth of soybean even under ER stress. This study highlights a vital target gene for future molecular breeding of stress-resistant soybean lines.

Increasing effective panicle number per plant (EPN) is one approach to increase yield potential in rice. However, molecular mechanisms underlying EPN remain unclear. In this study, we integrated map-based cloning and genome-wide association analysis to identify the EPN4 gene, which is allelic to NARROW LEAF1 (NAL1). Overexpression lines containing the Teqing allele (TQ) of EPN4 had significantly increased EPN. NIL-EPN4TQ in japonica (geng) cultivar Lemont (LT) exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT. Haplotype analysis indicated that accessions with EPN4-1 had medium EPN, medium grain number, and medium grain weight, but had the highest grain yield among seven haplotypes, indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield. Furthermore, accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations. Therefore, pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.

Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture.