Seedling emergence is a major determinant of stand establishment and subsequent yield formation in cotton (Gossypium hirsutum L.), yet it is highly vulnerable to early-season low temperature and soil salinity. This review synthesizes morphological, physiological, genetic, and mechanobiological advances to propose that hypocotyl elongation and apical hook development operate as a coordinated “elongation–protection” unit during cotton emergence. Hypocotyl cell expansion and cell-wall loosening generate the driving force needed for soil penetration, whereas hook curvature, produced by differential growth, buffers mechanical stress and protects the shoot apical meristem. We show that emergence failure under low temperature and salinity often occurs after germination, at the soil-penetration stage, when reduced elongation capacity, unstable hook curvature, or premature hook opening disrupt this integrated unit. Low temperature and salinity constrain emergence through convergent, multi-level mechanisms, including perturbed membrane/redox homeostasis, impaired energy metabolism, reduced cell-wall plasticity, and extensive rewiring of hormone biosynthesis, transport, and signaling. Recent advances further indicate that cell-wall integrity sensing, pectin remodeling, and energy–redox coordination are integral to the regulation of elongation and hook maintenance under stress. We propose a mechanistic framework linking hormone homeostasis, cell-wall mechanics, and morphogenetic output, in which auxin–ethylene coordination directs differential growth and hook curvature, gibberellins and brassinosteroids support elongation competence, and abscisic acid prioritizes stress responses. Cotton-specific evidence, including GhHLS1, GhSAL1, GhBRX family genes, and recent transcriptomic/network analyses, suggest that conserved regulatory modules are retained but rewired within a polyploid-specific regulatory architecture. Finally, we advance a unifying mechano-physiological concept of “resistance–driving force matching” and outline research priorities in quantitative mechanobiology, cotton-specific genetic regulatory network dissection, genetic variation mining, and integration with agronomic management and field phenotyping to improve stress-resilient cotton emergence.

Senescence allows plants to remove unnecessary tissues and recycle nutrients. Substantial work has focused on the senescence of aboveground tissues such as leaves; by contrast, the senescence of underground tissues has important functions in response to stresses such as drought. The root cortex transports water and provides structure to the root. Root cortical senescence (RCS) involves the programmed cell death of root cortical cells and allows the plant to adjust root system architecture and decrease the metabolic burden of maintaining root tissue. In this review, we synthesize current knowledge on RCS and its responses to drought stress. This review also examines the regulation of RCS at multiple levels and the differences in RCS between monocots and dicots. We further identify major challenges in characterizing RCS, understanding its mechanisms, and applying it in breeding, with an emphasis on bridging laboratory findings and field performance through genotype-by-environment analyses. Finally, we explore potential research directions and breeding targets for translating RCS into improved drought tolerance and yield stability in crops. This helps to clarify the physiological mechanisms of RCS, root system and leaf senescence, enhances the understanding of root system functions, and has significant theoretical value and practical significance for the prevention and control of crop premature senescence as well as the selection of anti-senescence varieties.

Gene-editing methods have significantly advanced genetic improvement and variety development in major food crops and have potential to make further major contributions to food security and human health. In this perspective, we analyze publication and patent data related to gene editing in rice (Oryza sativa), maize (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum) from 2013 to 2024. We survey the global research and development landscape, development trends, innovations in biotechnological breeding, and industrial applications of gene-edited crops, with particular attention to traits relevant to nutritional quality and health-related benefits. Our synthesis provides a reference for future research and industrialization of gene-edited crops.

Peanut (Arachis hypogaea L.) serves as a vital oilseed and food crop worldwide. Embryo abortion reduces seed set in peanut and significantly limits yields, but the mechanisms responsible have remained unclear. Here, we examined an ethyl methanesulfonate (EMS)-induced peanut mutant exhibiting early embryo abortion and a partially single-seeded pod phenotype. Cytological analysis indicated that seed abortion in the mutant begins at the proembryo stage, 7?d after flowering, with noticeable degeneration by 3?d after peg penetration into the soil (DAP), culminating in complete arrest by 10 DAP. Transcriptomic analysis identified 8778 differentially expressed genes (DEGs) during the transition from aerial to subterranean peg development in the mutant. These DEGs were significantly enriched for pathways such as MAPK signaling, auxin biosynthesis and transport, and calcium transport. Notably, we identified a premature stop codon mutation (C?>?T) in AhZAR1-4 of the mutant; this gene encodes a leucine-rich repeat receptor-like kinase. The mutation resulted in the truncation of the kinase and transmembrane domains of AhZAR1-4, leading to a loss of membrane localization and protein function. In yeast two-hybrid screening, AhZAR1-4 interacted with both AhIAA31 and AhBSK2. Heterologous overexpression of AhZAR1-4?_wt successfully rescued the seed-abortion phenotype of the Arabidopsis thaliana atzar1-4 mutant and increased seed size, whereas AhZAR1-4_mut expression did not. These findings identify AhZAR1-4 as a crucial regulator of seed development in peanut, making it a promising genetic target for improving pod yield and seed setting rate.

Although some lesion mimic mutants (LMMs) confer broad-spectrum disease resistance, their constitutive autoimmunity often penalizes plant growth and yield, limiting their application in crop breeding. Here, we report a novel strategy to overcome this trade-off in rice (Oryza sativa) by introducing a pathogen-inducible LMM gene variant, LRD6-6^E315Q. We first found that constitutive expression of LRD6-6^E315Q, a dominant-negative (DN) variant of the AAA-type ATPase gene LRD6-6, enhanced broad-spectrum resistance but inhibited plant growth, resembling the phenotype of the lrd6-6 mutant. To resolve this trade-off between disease resistance and growth, we screened a rice transcriptome and identified a rare inducible promoter, MIG6P that was specifically activated during early pathogen attack but maintained low activity under normal conditions, and was not inducible by abiotic stresses. We constructed a MIG6P:LRD6-6^E315Q cassette, introduced it into rice cultivar TP309, and developed rice lines with enhanced resistance to multiple diseases, including bacterial blight and fungal diseases rice blast and sheath blight without affecting growth or yield. Since promoters analogous to MIG6P and protein homologs of AAA-type ATPase LRD6-6 carrying potential DN effects occur in diverse plant species, this strategy may be widely applicable to improve disease resistance in other crop species.

The objective of this study was to determine how the rice receptor-like cytoplasmic kinase OsBSR1 positively regulates broad-spectrum disease resistance. Our results showed that OsBSR1 is induced upon infection by Magnaporthe oryzae and enhances rice immunity by negatively regulating the enzymatic activity of the sulfite oxidase OsSO1, while also affecting its stability. In agreement with this finding, overexpression of OsSO1 suppressed the reactive oxygen species burst, callose deposition, and defense gene expression, resulting in reduced resistance to M. oryzae. These results uncover a novel kinase–oxidase regulatory module underlying the coordination of immune responses and redox homeostasis in rice.

Grain filling is a pivotal determinant of wheat (Triticum aestivum L.) yield, relying on the efficient coordination of source–sink dynamics and assimilate partitioning. Jasmonic acid (JA) is widely involved in plant growth and development, and also plays an important role in resource allocation. However, it remains unclear if JA is involved in regulation of grain filling and assimilate transport in wheat. The objective of this study was to identify the roles of JA in regulating wheat grain filling and weight, by comparing cultivars, comparing superior and inferior grains of the same spikes, manipulating source–sink relationship by removing superior grains, and applying exogenous JA. The results showed the negative association between endogenous JA level and grain filling rate and final grain weight, irrespective of cultivars and source-sink treatments. JA increased assimilate retention in stems by reducing fructan mobilization and diminishing sucrose availability for grain development. In addition, JA suppressed sucrose unloading by reducing invertase (CWI and SAI) activities, and inhibited starch biosynthesis through reducing starch synthase (AGPase, GBSS and SBE) activities. These coordinated changes limited substrate sugar supply and starch accumulation, ultimately slowing grain filling rate. Overall, our findings reveal that JA changes the source–sink relationship, favoring carbon retention in vegetative tissues and reducing assimilate partitioning into grain.

Deeper understanding of the mechanism by which wheat responds to salt stress (SS) remains a major challenge due to the scarcity of available single-cell/nucleus transcriptomics resources. Here, in order to uncover the transcriptional patterns during the late stage of SS of different wheat cells, we performed single-nucleus RNA-sequencing (snRNA-seq) on roots and leaves of wheat seedlings under NaCl treatment for 7?d. Integrating snRNA-seq with bulk RNA-seq and physiological and biochemical indices measurement, the single-cell transcriptome atlas of wheat roots and leaves was constructed, and response patterns of cell types to SS were identified based on enrichment of differentially expressed genes for osmotic stress, ion transport, and oxidative stress. Moreover, several cell-type-specific salt-tolerant candidate genes were determined based on pseudotime analysis and functional validation, such as TaWRKY75-A in root hair cells, NICOTIANAMINE SYNTHASE (NAS) genes in root stele I cells, and dehydrin (DHN) genes in leaf fiber cells.

Stomatal movement is a crucial response of plants to drought stress. Several NAC transcription factors have been implicated in drought tolerance in maize seedlings, whereas the molecular mechanism by which they directly regulate ABA signaling components within the context of the four-cell stomatal complex remains unknown. In this study, we characterized ZmNAC16 in regulating drought resistance and stomatal closure in maize. Through phenotypic analysis of transgenic overexpression and gene-edited mutant lines, we assessed ZmNAC16 function in stomatal dynamics and drought tolerance. Overexpression of ZmNAC16 in transgenic maize resulted in increased leaf temperature, reduced stomatal conductance, decreased water loss, and enhanced drought tolerance, whereas gene-edited mutants exhibited opposite phenotypes. ZmNAC16 localized to the nucleus and acted as a transcriptional activator. Disruption of ZmNAC16 significantly downregulated key ABA signaling components, including ZmCIPK3 and ZmPP2C81, whose promoters were directly bound by ZmNAC16. Consistently, ZmNAC16 knockout mutants showed impaired ABA-induced stomatal closure, while overexpression lines displayed heightened stomatal sensitivity to ABA. Collectively, our findings demonstrate that ZmNAC16 integrates ABA signaling to regulate stomatal closure and drought tolerance in maize, positioning it as a promising target for enhancing crop resilience.

Heat shock transcription factors (HSFs) have roles in plant thermotolerance. However, the functional characterization and regulatory analyses of HSFs in maize remain limited. In this study, we cloned and characterized the previously uncharacterized maize HSF gene ZmHsfA5. Expression of ZmHsfA5 was significantly up-regulated under heat stress (HS). Overexpression of ZmHsfA5 enhanced thermotolerance in both maize seedlings and developing pollen by promoting proline accumulation and enhancing scavenging of reactive oxygen species. Conversely, ZmHsfA5 knockout mutants exhibited decreased thermotolerance. ZmHsfA5 physically interacted with the heat shock protein ZmHsp9. ZmHsp9 was significantly induced by HS, and transgenic experiments revealed that ZmHsp9 positively regulated thermotolerance, similarly to ZmHsfA5. Integrated analyses using CUT&Tag, RNA-seq, EMSA, and luciferase reporter assays demonstrated that ZmHsfA5 activated expression of oxidative stress-related genes by direct binding to heat stress elements in their promoters. Furthermore, ZmHsp9 stabilized the ZmHsfA5 protein under HS, thereby cooperatively enhancing transcriptional activation of the downstream target gene. These findings elucidate novel roles of the ZmHsfA5-ZmHsp9 module in maize thermotolerance and highlight its potential for enhancing adaptation to high-temperature environments.

Calcium-dependent protein kinases (CDPKs) function as key sensors of Ca²⁺ signals in plants; however, their roles in soybean-rhizobial symbiosis and biological nitrogen fixation remain poorly understood. This study demonstrates that GmCDPK14, a member of the soybean CDPK gene family, is specifically induced following rhizobial infection and is predominantly expressed in primary root tissues and nodules. Functional analyses revealed that GmCDPK14 plays a positive regulatory role in symbiotic nodulation. Loss-of-function mutants showed substantial decreases in nodule number, root dry weight, shoot dry weight, nitrogenase activity, and infection thread formation, whereas overexpression of GmCDPK14 produced the opposite effects. Transcriptomic analysis showed that GmRINRK1, a key symbiotic gene, was significantly downregulated in GmCDPK14-deficient lines. Moreover, overexpression of GmRINRK1 in the Gmcdpk14 mutant background partially rescued the nodulation defects. These results suggest that GmCDPK14 enhances soybean-rhizobium symbiotic nodulation by positively regulating GmRINRK1 expression, offering new insights into the role of CDPKs in controlling legume-rhizobium interactions.

Brassica napus L. is an allotetraploid plant that contains numerous boron (B) transporter genes, the functions of which are largely unknown. Here, we identified BnaC3.BOR1, a gene expressed in various tissues, including roots, stems, leaves, and floral organs. In yeast, BnaC3.BOR1 expression significantly reduces cellular B concentration. When grown in B-poor conditions, BnaC3.BOR1 mutation significantly lowered B concentrations in the xylem sap. BnaC3.BOR1 mutants exhibited stunted growth, including shorter roots, reduced shoot biomass, and leaf curling, compared to wild-type B. napus. In low-B soil, loss of BnaC3.BOR1 function resulted in shorter plant height and abnormal floral organ development with lower B levels, which ultimately reduced yield at the reproductive stage. Furthermore, BnaC3.BOR1 is expressed in multiple tissues, with specific expression in the regions below the nodes of stems. Mutants grown in B-poor soil exhibited stem cracking, and the B concentration in these cracks was lower than in wild-type plants. These findings indicate that BnaC3.BOR1 possesses the same conserved role in roots and flowers as previously discovered BOR1s, while having a distinct, specific role in stems. Our study provides a clear example of the functional diversification of B transporter homologous genes.

Photosynthesis is the basis of plant growth and development. It directly influences forage yield and quality; however, salt stress severely inhibits photosynthetic efficiency, accelerates leaf senescence, and reduces alfalfa yield and quality. Stay-green proteins (SGR) are important regulators of chlorophyll degradation and leaf senescence. RT-qPCR analysis of alfalfa seedlings revealed that MsSGR expression is significantly induced by salt stress in leaves and roots, suggesting its potential involvement in salt tolerance. Nevertheless, the specific role of MsSGR in the salt stress response of alfalfa remains unclear. We found that MsSGR is a negative regulator of salt tolerance in alfalfa. Compared with wild-type lines, MsSGR-overexpression (MsSGR-OE) lines exhibited more severe damage to photosynthesis, increased ROS accumulation, reduced antioxidant enzyme activity, and a higher mortality rate. Conversely, the MsSGR knockout (MsSGR-KO) line showed enhanced salt tolerance and survival rates. RNA-seq analysis revealed that the salt-sensitive phenotype of the MsSGR-OE lines was primarily affected by photosynthetic and antioxidant pathways. In addition, yeast two-hybrid, split luciferase complementation, and pull-down assays confirmed an interaction between MsSGR and MsMSRB5. Moreover, chlorophyll degradation assays indicated that MsMSRB5 can inhibit MsSGR-mediated chlorophyll degradation. MsMSRB5 overexpression significantly improved alfalfa salt tolerance. Based on these findings, we propose a mechanism for alfalfa salt tolerance mediated by the MsSGR-MsMSRB5 molecular module. This study enhances our understanding of how MsSGR regulates alfalfa salt tolerance and provides breeding strategies for developing salt-tolerant alfalfa varieties.

The objective of this study was to identify synthetic tetraploid wheats (STW) with tolerance to low nitrogen (LN) stress. We compared two STWs (S^shS^shA^mA^m and S^lS^lAA), their diploid parents, and natural tetraploid wheat (NTW) under normal and LN conditions. One excelled in early-stage LN resilience via root growth plasticity and efficient N uptake, while the other showed superior late-stage tolerance via photosynthetic retention and increased N storage. S-subgenome-encoded NPF/NRT2 transporter genes under LN stress may act as drivers of LN adaptation. In contrast, NTW showed a yield-stress tradeoff under LN. There is a possibility of boosting LN resilience in wheat breeding by targeting the S-subgenome of STWs.

Breeding resistant wheat (Triticum aestivum) cultivars is the most efficient way to manage wheat stripe rust, a highly destructive disease caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst). Therefore, the exploration of new resistance genes is ongoing. The resistance gene Yr85 confers protection against predominant Pst races in China at all stages of plant development. Here, we fine-mapped Yr85 to a 0.12?cM interval between allele-specific quantitative PCR markers XK1B-61 and XK1B-65, corresponding to a 1.76?Mb region on chromosome 1BS in the IWGSC RefSeq v2.1 reference genome (wheat cultivar Chinese Spring), using 5507 F₅ plants derived from heterozygous F₄ plants, themselves descendants of an AvS?×?AvSYr85NIL cross. Haplotype analysis and whole-genome resequencing suggested that Yr85 may be from a distant source. Moreover, agronomic trait evaluation indicated that Yr85 is located in a chromosomal region lacking linkage drag. Genotyping of 309 Chinese wheat cultivars and lines with a marker that cosegregated with Yr85 during fine mapping identified one cultivar possibly carrying the resistance gene. Our findings indicate that Yr85 has potential for use in wheat-breeding programs in China. This study lays the foundation for map-based cloning and marker-assisted selection of Yr85.

Aegilops mutica (genome T) harbors stripe rust resistance and is a potentially valuable genetic resource for broadening the genetic basis of disease resistance in common wheat. A dominant Ph1-suppression system in Ae. mutica promotes homoeologous pairing and recombination between wheat and alien chromosomes even in the presence of Ph1, providing a tool for alien gene mapping and introgression. In this study, we identified an all-stage stripe rust resistance gene, Yr1T, in Ae. mutica and mapped it to chromosome 1T using chromosome deletion lines of Langdon?×?Ae. mutica amphidiploids. Genetic stocks with an AABBTD genomic constitution were generated by crossing resistant amphidiploids with the susceptible common wheat cultivar MX169. We induced homoeologous recombination between chromosome 1T and wheat homoeologous group 1 chromosomes by leveraging the Ae. mutica Ph1-suppression system. Integrating cytological identification, molecular markers, and RNA-seq breakpoint mapping, Yr1T was delimited to an approximately 20?Mb physical interval near the centromere in chromosome arm 1TS. Screening of a 100-plant F₂ population yielded six recombinant plants with different breakpoints (6% recombination frequency), and a translocation line carrying Yr1T was developed. Collectively, these results demonstrated the high efficiency of the Ae. mutica Ph1-suppression system for alien gene mapping and targeted transfer, providing a practical reference for its application in wheat breeding.

Powdery mildew caused by the fungus Blumeria graminis f. sp. tritici (Bgt) is a prevalent disease that restricts wheat (Triticum aestivum) production globally. Diverse Bgt resistance genes and alleles are continually needed for wheat disease resistance breeding. We identified a wild emmer wheat (Triticum dicoccoides, WEW) introgression line, R53M, with effective resistance to Bgt isolate E09 starting at the two-leaf stage, during powdery mildew resistance assays in the greenhouse. Genetic analysis indicated that R53M carries a dominant powdery mildew (Pm) resistance gene, designated as PmR53M. We mapped PmR53M to the short arm of chromosome 2B, at the same approximate location as the resistance loci Pm68/MlIW39/PmWR183 from WEW. Sequence analysis revealed that the genetic interval containing the PmR53M locus includes Pm68d, an allelic variant of Pm68. We confirmed the resistance conferred by the PmR53M/Pm68d using virus-induced gene silencing (VIGS) and transgenic assays. This resistance results from the combined effect of two complementary nucleotide-binding and leucine-rich repeat (NLR) genes. In contrast to the all-stage resistance observed with Pm68 and MlIW39, PmR53M only conferred complete resistance to powdery mildew starting at the two-leaf stage, similar to PmWR183, which provides resistance at the three- and four-leaf stages. We developed co-segregating gene-based markers for the identification of PmR53M. The discovery of PmR53M enriches the Pm gene pool in wheat and should facilitate the genetic improvement of powdery mildew resistance.

Wheat yellow mosaic virus (WYMV) poses a significant threat to global autumn-sown wheat production. Growing wheat varieties with WYMV resistance is the most effective strategy for disease control. In this study, we fine-mapped a major WYMV resistance gene Ym5 (previously designated as QYm.njau-5A.1) in the Japanese wheat variety Xifeng. We delimited Ym5 to a 4.6?Mb linkage block (534.6–539.2?Mb in chromosome 5A) by genome-wide association study of 266 wheat accessions (excluding those carrying Ym1). Comparative genomic analyses revealed that resistant haplotypes, shared by Xifeng and European line ArinaLrFor, represent a putative alien introgression from Triticum monococcum. Twelve InDel and one KASP markers were developed and confirmed as diagnostic. Twenty-four recombinants were identified from a Xifeng?×?Yangmai 158 F₂ population consisting of 6882 individuals, and Ym5, flanked by markers ARI_106 and ARI_218, was narrowed down to a 1.1?Mb interval (534.8–535.9?Mb in ArinaLrFor). The use of Ym5 in Chinese breeding programs was traced to two sources: Xifeng and Australian variety Quality. Further investigation showed Ym5 introgression conferred no obvious yield penalty.

Pre-harvest sprouting (PHS) significantly reduces yield and quality in wheat (Triticum aestivum). One effective way to address this issue is to identify and deploy quantitative trait loci (QTL) for PHS resistance. In this study, we developed a recombinant inbred line (RIL) population derived from a cross between the PHS-resistant red wheat line ‘Shannong 0316’ (SN0316), which has strong seed dormancy, and the PHS-susceptible white wheat line ‘Gaoyou 9409’ (GY9409), which has weak seed dormancy, to map QTL for PHS resistance. We also mapped grain color, an important quality trait that is related to PHS. In five experiments, we identified thirteen QTL for PHS resistance, nine of which were detected in at least two experiments. QTL mapping identified seven QTL for grain color, three of which were also associated with PHS resistance. A comparison with previously reported QTL suggested that QPhs.sdau-1A, QPhs.sdau-5A, QPhs.sdau-6D, QPhs.sdau-7A, and QPhs.sdau-7B.1 are newly discovered QTL for PHS resistance, and that QGc.sdau-5A.1, QGc.sdau-5A.2, QGc.sdau-7A, and QGc.sdau-7B are newly discovered QTL for grain color. The three major QTL (QPhs.sdau-3A.1, QPhs.sdau-3D.1, and QPhs.sdau-1A) showed additive effects on PHS. We identified six elite lines with high PHS resistance, with three white wheat lines. We converted the single-nucleotide polymorphisms linked to the nine QTL into Kompetitive Allele-Specific PCR (KASP) markers and used them to genotype the RIL population and 192 elite breeding lines. QPhs.sdau-1A was associated with PHS resistance in the breeding lines, whereas the other QTL require further validation due to the low frequency of one genotype. Therefore, we dissected the genetic basis of the strong seed dormancy and PHS resistance of wheat line SN0316, identified QTL, obtained germplasm lines, and developed molecular markers for marker-assisted selection of PHS resistance, which should be valuable for breeding.

Plant height (PH) and aboveground biomass (AGB) are critical agronomic traits that determine the yield potential of maize (Zea mays L.). However, the application of genomic selection (GS) and genome-wide association studies (GWAS) in maize breeding is often hindered by the limitations of phenotypic data collection, which is typically characterized by low throughput and inadequate accuracy. To address this challenge, we employed an unmanned aerial vehicle (UAV) equipped with LiDAR and RGB cameras for high-throughput assessment of PH and AGB in a panel of 817 maize hybrids derived from 364 inbred lines over two growing seasons. Our results demonstrated that the integration of UAV-derived LiDAR point clouds with crop surface models (CSMs) enabled robust estimation of PH across multiple years (R²?>?0.90). Furthermore, a three-dimensional AGB estimation model was developed using UAV-derived PH and canopy coverage (CC), achieving high estimation accuracy (R²?>?0.83). Subsequently, the UAV-derived PH and AGB were utilized for GS and GWAS analyses. Replicated 10-fold cross-validation showed that the mean predictability was 0.504 for PH and 0.402 for AGB across eight commonly used GS models. Moreover, of the 66,066 potential crosses derived from the 364 inbred lines, the top 200 crosses selected for AGB showed up to twice the AGB of the bottom 200 crosses. Field validation demonstrated that the mean ear weight (EW) in the AGB top group was 39.0% higher than that in the bottom group. A total of 16 and 11 significant SNPs were identified by at least two GWAS methods for PH and AGB, respectively. Based on these SNPs, 81 candidate genes were functionally annotated, six of which were simultaneously associated with both traits. The candidate gene association analysis suggested that variations in the promoter region of ZmFLA9 may affect both traits. Overall, our study highlights the potential of UAV-based high-throughput phenotyping to accelerate maize genomic breeding by enabling rapid, precise, and large-scale trait assessment.

Soybean (Glycine max L.) is a global staple crop valued for its seeds, which contain about 40% protein in total weight, making them a rich source of plant-based protein. Enhancing soybean seed protein content (SPC) has long been a central focus of breeding research. In this study, we used a recombinant inbred line (RIL) population derived from the cross Dongnong L13?×?Henong 60 (RIL6013). We performed quantitative trait locus (QTL) mapping for SPC using a high-density genetic linkage map and IciMapping v4.2 software to identify and predict candidate genes associated with SPC. We employed the mrMLM method to detect significant quantitative trait nucleotides (QTNs) linked to SPC, followed by genomic selection (GS) based on these QTNs. We conducted simulation breeding, using genotypic data from significant QTNs and GS outcomes, to identify hybrid combinations for selecting high-protein soybean varieties. This analysis revealed 16 QTL associated with SPC, including a region containing the gene Glyma.02G250200 on chromosome 2. Genome-wide association study (GWAS) identified 37 significant QTNs, which we used as a single-nucleotide polymorphism (SNP) set for GS, together with the best linear unbiased prediction (BLUP) values of phenotypic data. We employed the five conventional statistical models BayesA, BayesB, BayesC, BayesLASSO, and GBLUP to perform genomic prediction. The prediction accuracy for all five GS models exceeded 0.65. Based on the five GS outcomes we devised five breeding schemes, followed by simulation breeding. The average genotypic values of the virtual progeny generated through these simulations were significantly higher than those of the parental populations. Simulation breeding identified 22 hybrid combinations optimal for high-protein selection. Of these, the line HN138 from the RIL6013 population was the parental line for multiple high-potential hybrid combinations and may thus represent the most suitable genetic background within RIL6013 for the breeding of cultivars with high protein content.

Peanut (Arachis hypogaea), a globally important oilseed crop, exhibits contrasting growth habits between wild species (prostrate) and cultivated varieties (erect or spreading), but the underlying mechanism is unclear. In this study, we performed quantitative trait locus (QTL) mapping of two recombinant inbred line (RIL) populations of peanut using SNP arrays and bulk segregant analysis, which identified qGH15 on chromosome 15 as a major QTL regulating growth habit. Fine mapping using KASP markers narrowed the candidate region to a 151-kb interval, while analysis of a residual heterozygous line (RHL) further delimited qGH15 to a 38-kb interval containing a single candidate gene, which we designated as AhGH15. Genotyping of a natural population revealed multiple types of polymorphisms in this gene associated with the erect habit in cultivated varieties. Phylogenetic and pedigree analyses demonstrated that these polymorphisms were recurrently and convergently selected during peanut domestication and breeding, with modern hybridization accelerating their dissemination. Transcriptome deep sequencing and gene co-expression analysis via WGCNA revealed polymorphism-specific patterns of transcriptome regulation, with co-expressed gene modules differentially active between accessions with erect or prostrate growth habits. These findings establish AhGH15 as a key determinant of peanut growth habit and highlight its complex selection history during peanut improvement.

In faba bean (Vicia faba L.), growth habit determines plant architecture and significantly influences flowering, podding patterns, and maturity. A recently identified semi-determinate germplasm exhibits favorable traits for mechanized harvesting and high yield potential, making it useful for developing a semi-dwarf faba bean ideotype with a high harvest index. To uncover the genetic basis of the semi-determinate growth habit, we investigated developmental differences in the shoot apical meristems (SAMs) of four faba bean germplasms with distinct growth habits using scanning electron microscopy. The phenotypic differences among these germplasms were attributed to variations in the duration of the overlap periods between vegetative and reproductive growth. Through bulked-segregant analysis (BSA) combined with linkage mapping in an F₂ population and a recombinant inbred line (RIL) population derived from Qingcan 17 (indeterminate)?×?RF25 (semi-determinate), we identified two quantitative trait loci (QTL): one located within a 3.73-Mb region on chromosome 5 (VfSdt1) and the other within an 8.68-Mb region on chromosome 1L (VfSdt2). We selected Terminal flower 1 (VfTFL1) as the candidate gene for VfSdt1, as a functional single nucleotide polymorphism (T-to-G) in this gene was found to be responsible for terminal inflorescence formation. VfTFL1 expression is downregulated before the SAM transitions into an inflorescence meristem and the subsequent termination of differentiation. VfFD was identified as the candidate gene for VfSdt2, as it harbors two nonsynonymous polymorphisms within its coding sequence that are associated with variation in growth habit. VfFD is specifically expressed in the shoot apex. These polymorphisms may promote vegetative growth of the SAM in the sdt1/sdt1 genetic background, resulting in a semi-determinate phenotype. These findings offer valuable insights for molecular design breeding aimed at developing semi-dwarf faba bean varieties.

Single-cell transcriptome sequencing (scRNA-seq) can reveal the roles of diverse cells in an organism, but accurately classifying cell subpopulations and their marker genes remains a challenge. Here, we present PhytoCell, an ensemble learning framework that combines feature selection engineering with machine learning to uncover cell markers and annotate cell subpopulations. We evaluated our approach on 120,000 cells from corollas of the dicotyledonous plant species coyote tobacco (Nicotiana attenuata) and eight tissues from the monocotyledonous plant species rice (Oryza sativa). Comprehensive evaluation across species and tissues demonstrated that PhytoCell effectively eliminates redundant information, identifies key cell markers, improves clustering performance, and accurately classifies cell subpopulations. Importantly, PhytoCell did not rely on prior biological knowledge for selecting cell markers, preserving the biological landscape of the original data. For broader accessibility, we developed a user-friendly web interface that provides convenient tools for users to access cell marker resources and perform predictions for cell type. PhytoCell is freely accessible at https://cgris.net/phyto. PhytoCell is scalable to different sizes of single-cell datasets, representing a valuable resource for precise identification in cell research.

We present Hi4GS, a hybrid feature selection (HFS) algorithm for selecting SNP subsets from high-dimensional genotypes to improve the prediction of genomic estimated breeding value (GEBV) under genomic selection (GS). Hi4GS combines feature importance weighting with quantity determining to construct a fused feature set from which it extracts an optimal feature subset for subsequent GS. In a study of wheat using four datasets covering 11 yield traits via large-scale GS models, the SNPs selected by Hi4GS increased the average predictive accuracy by over 82% than using all SNPs. Hi4GS was used to identify SNPs potentially affecting wheat yield, and SHAP-based interpretability was applied to explain the contributions of these SNPs and their potential interactions. Hi4GS can be used for assisting in improving the prediction accuracy of GS, wheat and other plants’ yield-associated SNPs identification, and target information for breeding chip development. The free R package Hi4GS is available at https://github.com/shgs19/Hi4GS.

Genomic selection (GS) has provided a comprehensive framework for efficient breeding by linking phenotypes to genome-wide markers. However, research on GS has predominantly focused on improving genotype-to-phenotype prediction models, often overlooking optimal cross design, which determines the potential of progeny selection and plays a critical role in crop breeding. In this study, an efficient GS framework, EMLGP (ensemble machine-learning for genomic prediction), was proposed for optimal cross design in crop breeding. EMLGP first employs machine-learning algorithms to train precise genotype-to-phenotype prediction models in a germplasm population and then integrates with genome simulations to predict optimal crosses in a breeding population. GS model training of 14 soybean traits demonstrated that EMLGP achieved superior performance, with the highest prediction accuracy (correlation coefficient) reaching 0.92. The prediction accuracy showed a maximum improvement of 35.85% over the classical GBLUP method. Further simulation studies confirmed that EMLGP exhibited robust performance under conditions of small-to-moderate sample sizes (300–5000), low-to-moderate trait heritabilities (0.4–0.6), and complex genetic architectures (100 causal loci). Validation using real data of rice, maize, cotton, sorghum, and switchgrass consistently affirmed EMLGP’s superiority, outperforming GBLUP and deep learning methods. Among the 14 soybean traits analyzed, 13 traits exhibited transgressive segregation potential in the progeny. Specifically, seed linolenic acid content in the northern China showed the highest recombination potential, exceeding the maximum parental value by 16.89%. In conclusion, EMLGP optimizes parental selection and phenotypic prediction, offering a robust framework for efficient, intelligence-driven crop breeding.

The objectives of this study were to identify canopy-level strategies for maximizing maize yield under high-density planting and to establish a 3D simulation framework for evaluating density-tolerant ideotypes. Based on a two-year field experiment varying varieties and planting densities, a 3D canopy photosynthesis-production model was developed. Results indicated that increased planting density reduced leaf area and light transmittance at the canopy bottom, which decreased intercepted photosynthetically active radiation and dry matter accumulation in one variety but increased them in another. Canopy structure accounted for more variation in yield than photosynthetic parameters. The higher radiation-use efficiency of MC812 under high planting density highlighted its superior density tolerance. These findings provide a quantitative basis for evaluating maize ideotypes and optimizing management strategies under intensive cultivation.

Rice ratooning produces a second harvest from the growth of axillary buds that remain on the stubble after the main crop is harvested. Stubble rolling after mechanical harvesting may regenerate roots and tillers. The objective of this study was to elucidate the relationships between axillary bud regeneration and yield formation in ratoon rice. The experimental approach was to measure yield and axillary bud regeneration traits under full-rolling and non-rolling treatments across three sites in Fujian Province, China over two years. Full-rolling increased grain yield by 7.59%–8.40% and the regeneration capacity of axillary buds by 9.45%–17.11%. Further analyses revealed that full-rolling increased the activities of carbon- and nitrogen-metabolizing enzymes in regenerating axillary buds, as well as the expression of genes involved in carbohydrate and nitrogen metabolic pathways. Mechanical harvesting combined with stubble rolling that presses rice stubble close to the soil surface induces a regenerative growth pattern that ultimately increases ratoon rice yield.

Extremely high temperatures (HT) caused by global warming pose serious threats to rice production. Potassium (K) is critical for plant stress tolerance, but its role in mitigating heat damage remains unclear. This study aimed to elucidate how high panicle K application affects mid-season rice HT tolerance in central China. A two-year field experiment grew two rice cultivars (heat-resistant Shanyou 63, SY63; heat-sensitive Liangyoupeijiu, LYPJ) under varying sowing dates and two K application levels (low K, LK, 50?kg K ha^?1; high K, HK, 90?kg K ha^?1) at the panicle initiation stage. Sowing date 1 (S1) and sowing date 2 (S2) increased the risk of heat stress exposure. Compared with late sowing (S3) under LK, early sowing reduced the yield in LYPJ by 41.3% (S1) and 51.3% (S2) in 2022, and by 35.4% (S2) in 2023, but did not affect the yield in SY63. Compared with LK in the same sowing date, HK increased yield by 44.7% (S1) and 61.5% (S2) in LYPJ in 2022, and by 30.6% (S2) in 2023, whereas it showed no significant effect on SY63 yield. Structural equation modeling analysis indicated that the yield loss could be primarily attributed to heat intensity at the panicle initiation and maturity stages. HK increased stomatal conductance and improved leaf water potential, thereby reducing canopy temperature by 1.2–1.3?°C at heading and 1.1–2.5?°C at maturity. Concurrently, HK enhanced carbohydrate supply and elevated enzyme activity for sugars utilization in anthers, collectively enhancing pollen viability and spikelet fertility. HK optimized source-sink traits via increasing leaf area index, specific leaf weight, spikelets per unit leaf area, post-anthesis translocation of stem dry matter (47.5%–48.9% in 2022 and 24.0% in 2023), and post-anthesis dry matter accumulation (33.0%–38.2% in 2022 and 19.0% in 2023). The study indicates that early sowing increases the risk of heat stress exposure for mid-season rice in central China, and the increase of panicle K application can mitigate yield loss by lessening canopy temperature and optimizing source-sink relationships.

Rice is a major food crop in China, and paddy fields are an important agricultural source of greenhouse gas (GHG) emissions. Achieving high yields while reducing GHG emissions is essential for national food security and agricultural carbon mitigation. Water-management during the rice season is widely used to reduce methane (CH₄) emissions; however, evidence of its effectiveness, particularly with respect to yield responses and CH₄ emissions before and after transplanting, remains inconsistent. To address this gap, we evaluated two tillage practices before transplanting and two irrigation regimes during the early tillering stage: aerobic tillage with controlled irrigation (AC), aerobic tillage with flooding (AF), conventional tillage with controlled irrigation (CC), and conventional tillage with flooding (CF, control). Field experiments were conducted in a high-latitude rice-growing region in China in 2024 and 2025. Across the two years of study, aerobic tillage significantly increased average rice yield by 6.3%, whereas controlled irrigation caused a slight decline. Compared with the CF, the AC treatment markedly reduced the peak dissolved CH₄ flux after the first drainage event by 66.4%–71.2% and lowered cumulative CH₄ emissions by 42.1%–51.7%. Consequently, AC achieved the lowest area-scaled GHG emissions (GHG_A) and yield-scaled GHG emissions (GHG_Y). These reductions were associated with a significantly greater abundance of methanotrophic genes under AC. In addition, aerobic tillage reduced average soil dissolved organic carbon (DOC) during the tillering stage by 11.8% across two study years. Overall, integrating aerobic tillage with controlled irrigation during the tillering stage provides an effective strategy for reducing CH₄ emissions while maintaining high yield and improving water-use efficiency in rice production.

The objective of this study was to identify the suitable blended controlled-release nitrogen (N) fertilizer strategies (BCRNFs) for soft wheat production and to elucidate its underlying physiological mechanisms. A two-year field experiment conducted at two sites using two N application rates and three N fertilizer types. In each N rate, the N fertilizer types include: CK, common urea applied twice; BCRNF1, which featured a single basal application of a 3:2 blend of 60-d and 180-d controlled-release N fertilizers, aiming to delay N release until later growth stages; BCRNF2, which featured a single basal application of 3:4:3 blend of urea, 60-d, and 180-d controlled-release N fertilizer, aiming to release N from early to middle growth stages. Compared with CK, BCRNF2 promoted starch synthesis and sucrose supply during the late grain-filling period of soft wheat, thereby increasing starch and amylose contents as well as the amylose-to-amylopectin ratio, while diluting protein and its component contents. The changes in these parameters mediated by BCRNF2 directly increased peak viscosity, trough viscosity, breakdown viscosity, final viscosity, and setback viscosity, ultimately improving soft wheat quality. BCRNF1 under reduced N application enhanced sucrose transport and starch synthesis capacity during the late growth period, which similarly supported the increase in starch content, the decrease in protein content, and the improvement of some key pasting characteristics. Therefore, BCRNF1 under reduced N conditions and BCRNF2 under conventional N conditions can enhance final grain quality and processing quality by increasing carbon metabolism during soft wheat grain filling, making them suitable for soft wheat production.

In the water-scarce North China Plain (NCP), choosing between straw mulching (SM) for surface conservation and straw incorporation (SI) for soil amelioration is a critical agricultural dilemma. However, their effects on soil water dynamics and crop productivity under different irrigation levels remain unclear. We conducted a two-year field experiment comparing SI and SM under three irrigation levels in winter wheat: no irrigation (I0), 60?mm irrigation at jointing (I60), and 60?mm irrigation at both jointing and heading (I60?+?60). Soil water dynamics were monitored, field-scale evapotranspiration (ET) was estimated using a water-balance approach, and aboveground dry matter, yield components, and water use efficiency (WUE) were measured. SM maintained higher topsoil water content early in the season, whereas SI generally showed greater changes in soil water storage (ΔSWS) and higher mean daily ET. Despite weaker early-stage surface water conservation, SI increased aboveground dry matter and grain yield by 5.2%–5.6%, resulting in 3.4%–4.0% higher WUE, with the advantage reaching 4.8%–4.9% under I60. This advantage was associated with improved early sink establishment (higher spike numbers) and superior ET conversion efficiency, requiring 18.8% less ET per unit dry matter increment. Under I60?+?60, the relative advantage of SI narrowed, indicating diminishing marginal yield response to additional ET. A conceptual model was developed to synthesize these straw return-irrigation interactions. We identified SI-I60?+?60 (highest yield) and SI-I60 (highest WUE) as optimal coupling modes, and recommend SI-I60 as the optimal management practice for this region, offering a practical strategy for winter wheat production under water-limited conditions.

Green manure is increasingly used to replace fallow because of its ecosystem benefits, yet its effects on subsequent crops remain uncertain in water-limited regions with high climatic variability. Accordingly, we conducted an eight-year field experiment on the semi-arid Loess Plateau to compare three cropping systems: winter wheat (Triticum aestivum L.) with summer bare fallow, soybean (Glycine max (L.) Merr.), or sorghum-sudangrass (Sorghum bicolor?×?S. sudanense). We quantified climatic resource use efficiency based on biomass and wheat yield responses across dry, normal, and wet years, and assessed associated changes in soil properties and grain quality. Green manure biomass inputs averaged 4035?kg ha^?1 for soybean and 6366?kg ha^?1 for sorghum-sudangrass, increasing total system biomass. Relative to the wheat–fallow system, precipitation, accumulated temperature, and radiation utilization efficiencies increased by 17.2%–18.5% in wheat–soybean and by 30.2%–35.9% in wheat–sorghum-sudangrass. However, in dry years, soybean and sorghum-sudangrass reduced wheat yield by 37.1% and 34.0%, respectively; in normal years, wheat yield tended to decline, but the difference was not significant, whereas the effect on wheat yield was overall neutral in wet years. Hierarchical partitioning showed stronger climatic control of interannual yield variability in the wheat–green manure system than in the wheat–fallow system. In addition, soybean increased soil available nitrogen and grain protein content, while sorghum-sudangrass led to greater increases in soil carbon and grain starch content; correspondingly, the soil quality index increased by 27.7% and 33.2%, respectively. Overall, replacing fallow with green manure increased interannual uncertainty in wheat yield responses, but improved soil properties support it as a viable option for sustainable rainfed management on the Loess Plateau.

Soybean (Glycine max (L.) Merr.), is one of the world’s most important oilseed and economic crops, yet its cell-biology-oriented gene-function studies remain hampered by low transformation efficiency and poor detection of fluorescent tags such as GFP. Researchers therefore routinely resort to heterologous systems like Arabidopsis or Nicotiana benthamiana, risking mis-localization and artifactual activity of soybean proteins and compromising physiological relevance. A robust, soybean-based platform is urgently needed. In this study, we introduce FLASH (Fluorescent Localization Assay for Subcellular in Hairy-root-derived callus protoplasts). Transgenic hairy roots expressing fluorescent proteins are bulked into callus, from which protoplasts are isolated in a single step and > 80% of cells display bright, stable fluorescence within 24?h. Using FLASH we monitored, in real time, light-induced assembly of GmCRY photobodies in both the nucleus and cytoplasm, and confirmed nuclear co-localization of GmCRY1b with STF1. FLASH offers a high-fidelity, high-throughput solution for subcellular localization, protein–protein interaction, and phase-separation studies of soybean proteins.

Wheat (Triticum aestivum L.) is one of the most important staple crops globally. Doubled haploid technology enables rapid development of pure lines and has been extended from maize to several other crop species. A key step in DH breeding is the identification of haploids from diploids, which requires accurate and convenient phenotypic markers. In this study, we generated two wheat haploid inducers carrying different markers by a one-step strategy. One harbored a dual fluorescent marker system consisting of eGFP and TagRFP, the other carried a RUBY reporter. Both markers enabled near 100% accuracy of haploid identification at the immature embryo, mature embryo, and germinating seedling stages. Moreover, both lines consistently exhibited a high and stable haploid induction rate (～20%). This study not only provides efficient wheat haploid inducers but also establishes a convenient pipeline for developing haploid induction systems in other crop species.

Haploid plants can improve the efficiency of cultivar development by shortening breeding cycles and increasing genetic gain per unit of time. The ability to produce androgenic haploids from seed can also permit development of approaches for rapid conversion of female parents of new F₁ hybrids to cytoplasmic male sterility (CMS). A method for rapid and routine cyto-conversion does not currently exist for tobacco (Nicotiana tabacum L.). In this research, we used gene editing, genetic engineering, and interspecific hybridization to develop an approach for identification of gynogenic and androgenic tobacco haploids produced from seed using a novel N. tabacum?×?N. tabacum intraspecific lethality system. An established genetic stock was observed to produce viable progeny after self-pollination. Progeny produced from crosses with normal N. tabacum genotypes exhibited greater than 99.7% intraspecific lethality, however. Amongst surviving seedlings were haploids believed to be produced via spontaneous parthenogenesis. The frequency of verified gynogenic haploids was observed to be approximately 1 in 5000 seeds, while the frequency of verified androgenic haploids was lower, approximately 1 in 50,000 seeds. Because of the fecundity of tobacco (～2500 seeds per pollination), these frequencies are high enough for use in practical plant breeding. A CMS version of the established genetic stock was demonstrated to be useful for converting an elite inbred line to CMS via androgenic haploidy.

Direct-seeded rice is a labor-saving and simplified planting pattern, usually accompanied by an increase in lodging risk. Improving the population structure has been demonstrated as an effective approach for solving this problem, and changing the sowing method is the most direct way to construct a reasonable population structure. The objective of this study was to compare the lodging characteristics of rice plants under three sowing or transplanting methods, including drone-ordered hill direct-seeding (DHDS), manual broadcast direct-seeding (MDS), and machine transplanting (MTR). In a two-year field experiment, DHDS significantly reduced the lodging index of the fourth (N4) internode from the top of the rice stem compared with MDS. Over the two years, DHDS and MTR decreased the field lodging rate by an average of 99.3% and 79.2%, respectively. This improvement in lodging resistance was mainly attributed to the enhanced breaking resistance caused by increased internode diameter and culm wall thickness, rather than changes in plant height or bending moment. DHDS also increased the cellulose and starch content of the N4 internode by 17.7% and 50.3% compared to MDS, respectively. Furthermore, there was no significant difference in grain yield among the different treatments. Our results suggest that DHDS can enhance lodging resistance of direct-seeded rice as a feasible sowing method without compromising yield, and it was noninferior to MTR in terms of yield and lodging resistance.