Light and nitrogen (N) are two critically environmental factors essential for plant survival, as they constitute the fundamental molecular framework of plant cells and significantly influence patterns of plant growth and development. Light is the driving force behind photosynthesis, a process that converts light energy into chemical energy stored as sugars. Additionally, light acts as a direct signal that can modulate plant morphogenesis and structural development. Nitrogen, as the most crucial mineral nutrient for plants, is a component of numerous biomolecules. It also functions as a signaling molecule, regulating plant growth and development. Moreover, light and nitrogen directly regulate the balance of carbon (C) and N within plants, affecting numerous biochemical reactions and various physiological processes. This review focuses on the interactions between light and nitrogen in physiological, metabolic, and molecular levels. We will also discuss the regulatory networks and mechanisms through which light and nitrogen influence C and N absorption and metabolism in plants.

Small signaling peptides, generally comprising fewer than 100 amino acids, act as crucial signaling molecules in cell-to-cell communications. Upon perception by their membrane-localized corresponding receptors or co-receptors, these peptide-receptor modules then (de)activate either long-distance or local signaling pathways, thereby orchestrating developmental and adaptive responses via (post)transcriptional, (post)translational, and epigenetic regulations. The physiological functions of small signaling peptides are implicated in a multitude of developmental processes and adaptive responses, including but not limited to, shoot and root morphogenesis, organ abscission, nodulation, Casparian strip formation, pollen development, taproot growth, and various abiotic stress responses such as aluminum, cadmium, drought, cold, and salinity. Additionally, they play a critical role in response to pathogenic invasions. These small signaling peptides also modulate significant agronomic and horticultural traits, such as fruit size, maize kernel development, fiber elongation, and rice awn formation. Here, we underscore the roles of several small signaling peptide families such as CLE, RALF, EPFL, miPEP, CEP, IDA/IDL, and PSK in regulating these biological processes. These novel insights will deepen our current understanding of small signaling peptides, and offer innovative strategies for genetic breeding stress-tolerant crops and horticultural plants, contributing to establish sustainable agricultural systems.

Plants produce many amino acid derivatives (AADs). Some have been used by humans as medicines and nutrients, but many also act as phytochemical signals in plant growth and stress tolerance. The fluctuating ecological environment poses a constant challenge to plant growth and development, and also presents significant obstacles to agricultural productivity. Plant AADs hold substantial potential for agricultural applications to increase plant resilience against diverse biological and environmental pressures. In this review, we present recent advances in elucidating the biological roles of plant AADs in plant growth and stress tolerance and outline strategies for discovering novel AADs and their regulatory networks in crops. The review aims to gain new insights into the functional properties of AADs in regulating plant growth and stress responses, which provides a valuable foundation for developing innovative AAD-based strategies to improve crop performance and resilience facing the ever-changing environment in the future.

Established allopolyploid species often contain specific gene(s) dedicated to suppressing the pairing of homoeologous chromosomes during meiosis. A longstanding question is whether such genes in allopolyploids with lower ploidy levels can retain full functionality when the ploidy level rises following the addition of a new subgenome during outcrossing. Here, we addressed this question by generating a synthetic allohexaploid wheat species, Triticum kiharae (GGAADD), by crossing the allotetraploid Triticum timopheevii (GGAA) to the diploid Aegilops tauschii (DD), followed by colchicine-induced chromosomal doubling. The gene Pairing homoeologous 1 (Ph1) inherited from T. timopheevii was likely hypofunctional in nascent T. kiharae, as evidenced by irregularities during meiotic chromosome pairing and organismal numerical and structural chromosome variation in selfed progeny populations. The allohexaploidization event also induced substantial rewiring of gene expression among homoeologs and nonadditive gene expression, leading to distinct predicted biological functions for differentially expressed genes (DEGs) when they were partitioned into the subgenomes. F₁ hybrids from a cross between T. kiharae and bread wheat (T. aestivum, BBAADD) were male-sterile but female-fertile, confirming intrinsic postzygotic reproductive isolation between the two species while enabling backcrossing of these sterile F₁ hybrids to bread wheat. These features provide a feasible route to simultaneously introgress standing congeneric genetic variations from both T. timopheevii and Ae. tauschii, as well as heritable de novo variations that have arisen in T. kiharae into bread wheat.

CALCINEURIN B-LIKE PROTEINS (CBLs) function in osmotic stress responses, root morphogenesis and ion uptake in various plants such as Arabidopsis. However, the roles of OsCBLs in regulating root growth in rice (Oryza sativa), whose root morphology and growth environment strongly differ from those of Arabidopsis, are unknown. Here, we demonstrated that OsCBL3 functioned as a calcium sensor to regulate primary and lateral root development in rice. OsCBL3 interacted with OsCIPK31 in vivo and in vitro, and the loss of function of OsCBL3 or OsCIPK31 resulted in shorter roots and diminished lateral root growth. Overexpression of OsCIPK31 compensated for the root growth defects of OsCBL3 knockout mutants. These results demonstrated that the OsCBL3-OsCIPK31 module coordinated root development via the abscisic acid (ABA) and auxin pathways, as ABA inhibitors and low auxin concentrations partially rescued the short-root phenotype of their respective knockout lines. CYCLOPHYLIN 2 (OsCYP2), a key factor in lateral root initiation and root growth maintenance, was phosphorylated by OsCIPK31, and knockout of OsCYP2 in OsCIPK31 overexpression lines resulted in a phenotype similar to that of OsCYP2 single knockout lines. Therefore, the OsCBL3-OsCIPK31 module functioned in ABA and auxin signal transduction, ensuring proper root growth. OsCIPK31, activated by OsCBL3, then phosphorylated OsCYP2, which drove primary and lateral root development. These results establish a new module regulating primary and lateral root development in rice.

Flowering time (or heading date) is a crucial agronomic trait for the adaptation of rice to specific growing regions and seasons. Although many flowering time-related rice genes have been identified and functionally characterized, continuing in-depth research is revealing how transcription of these genes is regulated. In this study, we determined that a basic leucine zipper transcription factor (OsbZIP40) and its homologous protein (OsbZIP12) participate in the control of flowering time. Overexpression of OsbZIP40 delayed flowering. Double mutants in which both OsbZIP40 and OsbZIP12 were knocked out exhibited an early-flowering phenotype under both long-day and short-day conditions. However, there was no difference in the heading date between the wild-type and each single mutant. These results suggest that OsbZIP40 functions as a flowering suppressor. Both OsbZIP40 and OsbZIP12 bound directly to the Ehd1 promoter and repressed its expression. Furthermore, MOTHER OF FT AND TFL1 (OsMFT1) interacted with OsbZIP40/OsbZIP12 and enhanced their repressive effects on Ehd1 expression. Based on the data, we present a transcriptional regulatory mechanism in which OsbZIP40 and OsbZIP12 interact with OsMFT1 and modulate Ehd1 expression to delay flowering. Our findings provide relevant insights into the molecular mechanisms regulating flowering time in rice.

The early responsive to dehydration-like (ERDL or ERD) subfamily, subclade within the monosaccharide transporter (MST) superfamily, is crucial in the regulation of growth and seed yield in Arabidopsis. Here, we identified OsERD5 as an AtERDL6 homologue and explored the function of OsERD5. We found that OsERD5 overexpression significantly enhanced the tiller number and grain yield of rice. OsERD5 was widely expressed in aboveground tissues, encoded a tonoplast-localized protein, and exhibited transport activities for fructose, glucose and mannose when expressed in yeast. Expression character assay revealed that OsERD5 mediated hexose efflux across tonoplasts and participated in maintaining the diurnal rhythm-regulated intracellular hexose homeostasis. Additional physiological and molecular evidence showed that OsERD5 overexpression promoted vacuolar glucose efflux, enhanced sucrose synthesis and transport, increased sugar content in the shoot base, and promoted rice tillering by activating the synthesis of cytokinin simultaneously repressing strigolactone and gibberellin signaling. This study elucidates the function of OsERD5 and the mechanism underlying the overexpression of OsERD5 increasing rice tillering and yield.

Rice grain size and chalkiness are important traits that influence grain yield and quality, respectively. Mining of genes for grain yield and appearance quality and clarification of their action modes are of great importance in rice breeding. In this study, a rice protein disulfide isomerase-like enzyme PDIL2-3 was characterized. Expression analysis revealed that PDIL2-3 was highly expressed in endosperm and spikelet hulls. The PDIL2-3-cri lines generated by CRISPR/Cas9 technology exhibited a chalky grain phenotype with altered storage substance accumulation and increased grain size and weight, whereas exactly opposite results were obtained for PDIL2-3 overexpression lines. Cytological experiments revealed that PDIL2-3-cri increased rice seed length mainly by increasing the cell number and rice seed width mainly by increasing the cell size in grains, implying that PDIL2-3 regulates the grain size by influencing both cell division and expansion of spikelet hulls. Further flow cytometric analysis validated that PDIL2-3 has a negative effect on cell proliferation, preventing DNA duplication and cell division in spikelet hulls. Moreover, qRT-PCR results showed that the expression levels of genes related to cell cycle and storage substance synthesis were significantly changed in PDIL2-3-cri transgenic lines. Thus, our results indicated that PDIL2-3 plays a pivotal role in influencing grain size and quality of rice by affecting cell division/expansion and storage substance accumulation, providing new insights into the function of PDIL family members in rice and enriching the genetic resources for rice breeding.

Salinity tissue tolerance is a key trait that confers adaptive potential in halophytic species. The aim of this study was to understand the mechanistic basis of salinity tissue tolerance in the Oryza coarctata, a halophytic wild relative of cultivated rice Oryza sativa, to be then used as novel targets for improving salinity stress tolerance of O. sativa. Salinity led to ∼80% decline in mesophyll cell viability in cultivated rice, whereas only 15% reduction was observed in the wild rice. In response to NaCl treatments, mesophyll cells of O. coarctata showed less Na⁺ uptake and better K⁺ retention than cultivated rice. Pharmacological experiments suggested that salinity-induced Na⁺ uptake and K⁺ loss in O. coarctata were mediated by non-selective cation channels (NSCCs) while K⁺ loss in cultivated rice was mediated predominantly by GORK (guard cell outward-rectifying K⁺) channels. Salt treatment resulted in a depolarization of the plasma membrane (PM) in O. sativa. In contrast, O. coarctata had NaCl dose-dependent hyperpolarization in the mesophyll cells, due to its higher preference for Cl⁻ uptake. This difference in plant ionic relations was partially attributable to differences in transcriptional expression levels of Potassium transporter 1 (AKT1), Salt overly sensitive 1 (SOS1), Sodium transporter OsHKT1;4, and Chloride channel (OsCLC1). It is concluded that O. coarctata possesses a strong ability to discriminate between Cl⁻ and Na⁺ uptake (a trait lacking in cultivated rice) and use it to maintain negative membrane potential (MP) values without activating H⁺-ATPase, thus enabling more efficient K⁺ retention in mesophyll with low energy costs. The above traits should be considered as potential targets in the rice breeding program for salt tolerance enhancement.

Low- temperature (LT) stress is a significant abiotic stress in rice growth, especially under direct seeding cultivation, where low temperatures can significantly affect seed germination and seedling growth of direct-seeded rice, thereby impacting the final yield of rice. In this study, we have identified a trehalose synthesis pathway gene, trehalose-6-phosphate phosphatase 3 (OsTPP3), involved in the regulation of low-temperature (LT) germination in rice, as well as its upstream regulatory factor, the ABA signaling pathway gene OsbZIP23. LT stress induced the accumulation of ABA by upregulating the expression of OsNCED3. Consistently, the overexpression of OsNCED3 significantly inhibited seed germination under LT. RT-qPCR experiments found that the expression of OsbZIP23 was also significantly induced under LT stress and ABA treatment. Overexpression of OsbZIP23 has increased the sensitivity to LT stress of rice seed, resembling the phenotype of OsNCED3 overexpressing seeds. Furthermore, both LT stress and exogenous ABA treatment increased the trehalose content in WT seeds by upregulating the expression of OsTPP3. Enhancing the expression of OsTPP3 or application of exogenous trehalose have significantly increased the sensitivity to LT stress during seed germination. Transcriptional activation and yeast one-hybrid assays demonstrated that OsbZIP23 bound to the promoter of OsTPP3 and activated its expression, which was intensified by LT stress or the application of ABA. Our study discovered an ABA-dependent OsbZIP23-OsTPP3 module that responds to LT stress, inhibiting seed germination under LT conditions by increasing trehalose accumulation, thus might balance the growth and stress resistance and provide a new insight into the genetic improvement of rice cultivars with better LT germination performance.

Male reproductive development is necessary for the alternation of the life cycle in angiosperms. Due to functional redundancy of genes in the allohexaploid genome of common wheat, there are only two loci of recessive nuclear genic male sterility (GMS) mutations reported in wheat. Here, we report a new wheat recessive GMS gene, TaMs6, which encodes a GDSL esterase/lipase protein (GELP). TaMs6 is predominantly expressed in the anther during meiosis and the unicellular microspore stage, especially in meiotic cells (MCs), dyad cells, tapetum, and middle layer. The loss of TaMs6 function leads to male sterility, likely due to the downregulation of some pollen development-related genes and changes in lipid composition during meiosis. The ms6 mutant and Ms6 gene can potentially be utilized for developing commercial-scale hybrid wheat breeding systems. We also systematically analyzed the GELP gene family in wheat, providing a comprehensive understanding of the TaGELP family and offering valuable references for in-depth genetic studies. Additionally, we discovered the nonallelic noncomplementation of two male-sterile mutants, which presents an interesting and promising research direction.

Seed maturation is a critical development transition and it largely affects the final yield and quality of crops. Abscisic acid (ABA)-activated sucrose-non-fermentation kinase subfamily 2 (SnRK2s) constitute a well-known regulatory network that modulate seed maturation in Arabidopsis; however, the underlying genetic and regulatory mechanisms in cereal crops remain largely unknown. Here, we found that ABA levels exhibited two distinct peaks during kernel development in maize, corresponding to the lag and maturation phase, respectively. Integrated transcriptome and proteome profiling of kernels treated with exogenous ABA at the pre-maturation stage suggested that the second peak of ABA acts as a trigger for kernel maturation program. Knockout of ZmSnRK2s demonstrated that subclass III ZmSnRK2s are required for kernel maturation in maize, and the loss-of-function of subclass III ZmSnRK2s showed a disruption in kernel dehydration and dormancy. We identified a conserved ABA-SnRK2-bZIP signaling pathway mediating this process in maize. Additionally, ZmSnRK2.10 overexpression accelerates kernel dehydration during maturity, achieving reduced kernel moisture content (KMC) at physiological maturity (PM). Overall, our findings establish ABA-activated SnRK2s as central regulators of kernel maturation in maize and provide valuable genetic resources for breeding maize varieties with low moisture content at harvest.

Maize (Zea mays L.) is one of the world's most important staple crops, and is used for manufacturing food, feed, and industrial products. A key factor in maize yield is the grain weight, which directly influences productivity. In this study, we revealed the role of smk23 in maize kernel development. The ethyl methanesulfonate mutant smk23 is characterized by substantially reduced kernel weight. Through map-based cloning, smk23 was found to be located on Chr5 and encode a putative B-type response regulator, ZmRR5. A change from G to A occurs in the coding sequence of ZmRR5, resulting in the early termination of smk23. In Arabidopsis, B-type response regulators are involved in cytokinin signaling. Histological analysis and in situ hybridization of the mutant revealed abnormal endosperm development, particularly in the basal endosperm transfer layer (BETL), a specialized tissue critical for nutrient transport from the maternal tissues to the developing kernel. ZmRR5 positively regulates key genes involved in BETL development and function, including MRP1 and TCRR1. Furthermore, RNA sequencing revealed that several genes closely linked to BETL development, including BETL2, MEG1, and MN1, were significantly downregulated in smk23. These genes are essential for nutrient transport, tissue development and signal transduction. In addition, haploid analysis of ZmRR5 revealed natural variations (Hap 2) that may contribute to the increased kernel yield. Disruption of ZmRR5 function in smk23 leads to defects in BETL development, impairing its ability to transport nutrients, and ultimately resulting in a smaller kernel size. This study provides new insights into the molecular mechanisms through which ZmRR5 regulates maize kernel development and offers potential strategies for improving grain yield.

Improving protein quality and grain yield traits coordinately is an important goal for crop breeding. To date, many protein-quality or grain-yield regulation genes have been identified. However, the genetic strategies integrating these genes in good-protein-quality and high-yield crop breeding practice are far from established. Here, we characterized the functions of the MADS domain-containing protein ZmMADS8 and Zea mays G protein gamma subunit 1 (ZmGG1) in regulating protein quality and grain yield of maize. ZmMADS8 positively regulates zein protein accumulation and negatively regulates non-zein protein and lysine levels in kernels by interacting with ZmMADS47 to promote the transcriptional activation of Opaque2. Additionally, ZmMADS8 regulates starch content of kernels by targeting genes involved in starch biosynthesis. ZmGG1, a putative interactor of ZmMADS8, negatively regulates kernel number with a trade-off effect on kernel starch accumulation. The mads8;zmgg1 double mutant improved protein quality by attenuating zein biosynthesis and increasing essential lysine level, and increased grain yield by increasing kernel number, compensating for decreased starch biosynthesis. Our findings revealed the biological function of ZmMADS8 and ZmGG1 in regulating protein quality and yield related traits and suggested a genetic strategy by direct editing of ZmMADS8 and ZmGG1 to improve grain yield and protein quality simultaneously.

Small RNAs (sRNAs) are essential for regulating plant growth and development, and they possess the notable ability to travel long distances within organisms to regulate target gene expression. Our study examined the dcl2 mutant, a key enzyme in sRNA biogenesis, to determine the role of the DCL2 protein in sRNA synthesis and to identify mobile sRNAs under DCL2 regulation. Through grafting experiments between dcl2 mutants and wild-type soybean plants, coupled with sRNA sequencing, we identified 14,105 sRNAs significantly affected by DCL2 and discovered 375 mobile sRNAs under its regulation. Degradome analysis provided deeper insights into the regulatory effects of these mobile sRNAs on their target genes, enabling us to understand their potential influences on plant development and stress responses. Leveraging the systemic movement of sRNAs from roots to shoots, we propose a novel strategy for manipulating gene expression in aboveground tissues. Overall, our research findings not only deepen our understanding of the complex regulatory networks involving mobile sRNAs regulated by DCL2, but also provide a new strategy for gene regulation, which could have a positive impact on agricultural biotechnology.

In plants, numerous non-Mendelian inherited dominant effects, including over-, incomplete-, and co-dominance, are frequently observed, yet they remain insufficiently understood. A novel phenotype has been identified in specific soybean transformants overexpressing a single 35S::GmFT2a copy: super-early flowering dominance is exclusively observed in hemizygotes, not in homozygotes. Homozygous individual exhibits siRNA-mediated DNA methylation, causing epigenetic transcriptional silencing, whereas no such effect occurs in hemizygotes. Intriguingly, two distinct rounds of DNA methylation establishment occur, each mediated by a different mechanism. The homozygotes that derived from the hemizygous mother plants carrying 35S::GmFT2a locus was associated with the initiation of CHH-context DNA methylation at 35S promoters mediated by 21 and 22 nucleotide (nt) siRNAs. Subsequently, 24 nt siRNAs contribute to additional CHG- and CG-context DNA methylation at 35S promoters during the homozygosity of genes in plants already homozygous in maternal lineage. Reducing DNA methylation levels can be achieved by generating a hemizygous genotype through a crossing experiment with a recessive genotype. This research has unveiled a phenomenon: hemizygote-dependent dominance resulting from transcriptional silencing in homozygote offsprings. It provides new insights into the molecular mechanism underlying dominant effects.

The Brassica polima cytoplasmic male sterility (pol CMS) line causes complete and stable sterility and is most extensively used in breeding. The regulatory pathway, however, is not clear. In this work, we studied molecular interaction among several key genes involved in pol CMS. Firstly, we found that the multicellular organelle RNA-editing factor protein (Bna.MORF1) interacted with the pol CMS-restorer protein RFP using the yeast two-hybrid system. Secondly, knock down of Bna.MORF1 using CRISPR/Cas9 editing resulted in sterile transgenic lines. The function of the pol CMS sterility gene orf224 was further confirmed by ectopic expression of the gene in both Arabidopsis and Brassica. Furthermore, using CRISPR/Cas9 we determined that an anther-specific proline-rich protein (APG) was also involved in sterility. We propose a working model for pol CMS in Brassica napus that may expedite the utilization of this popular CMS line in Brassica breeding.

Red petal spots are beneficial for attracting cotton pollinators and producing hybrid seeds, and the anthocyanin pathway is generally regarded as a metabolic cause of petal coloration. The current study identified an MYB-encoding gene (Gar07G09390, GaMYB) as a candidate gene involved in cotton coloration by map-based cloning, and this MYB could positively regulate a candidate glutathione S-transferase gene (Gar07G08900, GaGST). To unveil potentially involved genes within the GaMYB-regulating-GaGST route, color metabolites of both GaMYB- and GaGST- virus-induced gene silencing (VIGS) petals were investigated, revealing that they were largely glycosyl-decorated flavonoids. Accordingly, a transcriptomic survey of both VIGS petals identified a glycosyl-transferase gene (GaGT, Gar02G15390). Notably, this GaGT is adjacent to one of the genome-wide association study loci concerning petal spots in Gossypium arboreum, and it is also positively regulated by GaMYB. This new regulatory route including both GST and GT regulated by MYB is conserved among the three cotton species examined in this study (Gossypium arboreum, Gossypium hirsutum, and Gossypium barbadense). Accordingly, comprehensively evaluating the influence of these candidates and their homologs on cotton coloration may provide a more in-depth understanding of cotton coloration, ultimately facilitating the breeding of more colorful cotton.

Mitogen- activated protein kinase (MAPK) cascades are crucial in plant responses to various stresses. While the positioning of MAP4Ks within the canonical MAPK signaling module in plants remains controversial, emerging research continues to shed light on their functional roles. However, information on the MAP4K gene family in pepper (Capsicum annuum) is still limited. In this study, seven putative MAP4K genes (designated as CaMAP4K1-CaMAP4K7) were identified from the pepper genome, each containing a conserved serine/threonine kinase domain. These genes were differentially expressed across various pepper organs, with CaMAP4K3 exhibiting consistently high expression in all organs and significant induction under drought stress. Kinase assays revealed that CaMAP4K3 is an active kinase whose activity is enhanced by drought and salt stress. Functional studies showed that silencing CaMAP4K3 enhanced drought resistance in pepper plants, reducing transpirational water loss and increasing leaf temperatures. Conversely, CaMAP4K3 overexpression in tobacco and Arabidopsis reduced drought tolerance, as evidenced by increased wilting and transpirational water loss. Additionally, CaMAP4K3-overexpressing Arabidopsis plants exhibited reduced sensitivity to abscisic acid (ABA) during seed germination and seedling growth. Collectively, these results suggest that CaMAP4K3 impairs drought resistance in pepper plants and potentially affects seed germination and seedling growth through the regulation of ABA signaling.

Efficient and accurate identification of candidate causal genes within quantitative trait loci (QTL) is a significant challenge in genetic research. Conventional linkage analysis methods often require substantial time and resources to identify causal genes. This paper proposes a QTG-LGBM method for prioritizing causal genes in maize based on the LightGBM algorithm. QTG-LGBM dynamically adjusts gene weights and sample proportions during training to mitigate the effects of class imbalance. The method prevents overfitting in datasets with small samples by introducing a regularization term. Experimental results on maize traits, including plant height (PH), flowering time (FT), and tassel branch number (TBN), demonstrated that QTG-LGBM outperforms the commonly used methodsQTG-Finder, GBDT, XGBoost, BernoulliNB, SVM, CNN, and ensemble learning. We validated the generalization of QTG-LGBM using Arabidopsis, rice, Setaria, and sorghum. We also applied QTG-LGBM using reported QTL that affect traits of maize PH, FT and TBN, and FT in Arabidopsis, rice, and sorghum, as well as known causal genes within the QTL. When examining the top 20% of ranked genes, QTG-LGBM demonstrated a significantly higher recall rate of causal genes compared to random selection methods. We identified key gene features affecting phenotypes through feature importance analysis. QTG-LGBM is available at http://www.deepcba.com/QTG-LGBM.

Pigment accumulation is an important trait related to wheat domestication, but there remains a limited understanding of its molecular mechanism. The genetic control of the red glume trait by a dominant allele, Rg-B1, on 1BS was reported in the last century, but the underlying gene and its molecular basis remained elusive. Here, we identified TraesTSP1B01G005700 (G57) encoding an R2R3-MYB transcription factor (TF) as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study (GWAS), bulked segregant RNA-sequencing (BSR-Seq), map-based cloning, and RNA-seq. The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity. Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57, resulting in the red glume phenotype. G57 could bind to the promoters of anthocyanin synthesis genes TaCHS, TaF3?H, and TaUFGT, activating their expression and contributing to anthocyanin accumulation in wheat glume. G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight, thereby causing increased grain weight. Our research offers a better understanding of the molecular basis of red glume in bread wheat.

Spike length (SL) is an important factor affecting yield in wheat (Triticum aestivum L.). Here, a recombinant inbred line (RIL) population derived from a cross between Shannong 4155 (SN4155) and Shimai 12 (SM12) was used to map quantitative trait loci (QTL) controlling SL. A QTL, qSL2B, on chromosome 2B was identified in all experiments and explained 9.92%-12.71% of the phenotypic variation. Through transcriptome and gene expression analysis, we identified a gene encoding Elongation Factor 1-alpha (TaeEF1A) as the candidate gene for qSL2B. Genome editing of TaeEF1A demonstrated that TaeEF1A positively regulates SL, spikelet number per spike (SNS), and grain number per spike (GN). Transcriptome analysis showed that TaeEF1A may affect the protein translation process and photosynthesis to regulate spike development. We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in TaeEF1A, with Type I, Type II, and Type III being the major haplotypes. Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as Type I and Type II haplotypes, respectively, with Type III not detected. Comparison of SL, SNS, and GN between the Type I and Type II haplotypes revealed that the Type I allele can increase SL, SNS, and GN simultaneously, and is thus preferred for use in wheat molecular breeding efforts to increase SL, SNS, and GN.

Emerging new races of wheat stem rust (Puccinia graminis f. sp. tritici) are threatening global wheat (Triticum aestivum L.) production. Host resistance is the most effective and environmentally friendly method of controlling stem rust. The stem rust resistance gene Sr59 was previously identified within a T2DS·2RL wheat-rye whole arm translocation, providing broad-spectrum resistance to various stem rust races. Seedling evaluation, molecular marker analysis, and cytogenetic studies identified wheat-rye introgression line #284 containing a new translocation chromosome T2BL·2BS-2RL. This line has demonstrated broad-spectrum resistance to stem rust at the seedling stage. Seedling evaluation and cytogenetic analysis of three backcross populations between the line #284 and the adapted cultivars SLU-Elite, Navruz, and Linkert confirmed that Sr59 is located within the short distal 2RL translocation. This study aimed physical mapping of Sr59 in the 2RL introgression segment and develop a robust molecular marker for marker-assisted selection. Using genotyping-by-sequencing (GBS), GBS-derived SNPs were aligned with full-length annotated rye nucleotide-binding leucine-rich repeat (NLR) genes in the parental lines CS ph1b, SLU238, SLU-Elite, Navruz, and Linkert, as well as in 33 BC₄F₅ progeny. Four NLR genes were identified on the 2R chromosome, with Chr2R_NLR_60 being tightly linked to the Sr59 resistance gene. In-silico functional enrichment analysis of the translocated 2RL region (25,681,915 bp) identified 223 genes, with seven candidate genes associated with plant disease resistance and three linked to agronomic performance, contributing to oxidative stress response, protein kinase activity, and cellular homeostasis. These findings facilitate a better understanding of the genetic basis of stem rust resistance provided by Sr59.

One-third of the global population is affected by micronutrient deficiency, particularly folate. Although folate synthesis has been relatively well characterized, few folate-related genes in maize have been cloned, and the molecular mechanism regulating folate synthesis in maize remains unclear. In this study, transcriptome and proteome analyses of three waxy maize inbred lines with high, medium, and low folate contents were performed to identify key genes controlling folate biosynthesis. Pairwise comparisons revealed 21 differentially expressed genes and 20 differentially expressed proteins potentially associated with folate biosynthesis in the three lines. Six key folate-associated genes, ZmMocos2, ZmGGH, ZmADCL2, ZmCBR1, ZmSHMT, and ZmPurH, were identified. These genes encode enzymes that potentially function in folate biosynthesis. Functional validation of one of these genes, ZmADCL2, using an EMS mutant (Mut9264) showed that a 4-base insertion in an exon increased the folate content of fresh maize kernels 1.37-fold that of the wild type. ZmADCL2 was considered a potential target for generating maize lines with higher folate content. KEGG enrichment analysis of differentially expressed genes and proteins showed that several pathways in addition to folate biosynthesis were likely indirectly involved in folate metabolism and content (e.g., glycine, serine, and threonine metabolism; purine metabolism; cysteine and methionine metabolism; alanine, aspartate and glutamate metabolism; glutathione metabolism; and pyruvate metabolism. The transcriptome and proteomic data generated in this study will help to clarify the mechanisms underlying folate accumulation and aid breeding efforts to biofortify maize with folate.

The genetic basis for Gossypium hirsutum race latifolium, the putative ancestor of cultivated upland cotton, emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown. Here, we reported a high-quality genome assembly of G. latifolium. Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes, including the expansion of photosynthesis-related gene groups in G. latifolium compared with other races and the pivotal contribution of structural variations (SVs) to G. hirsutum domestication. Based on the resequencing reads and constructed pan-genome of upland cotton, co-selection regions and SVs with significant frequency differences among different populations were identified. Genes located in these regions or affected by these variations may characterize the differences between G. latifolium and other races, and could be involved in maintenance of upland cotton domestication phenotypes. These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.

The flowering time is a key trait that determines adaptation, yield and quality of crops. Adlay, a traditional cereal crop, has developed a distinctive agricultural industry in Southwest China and Southeast Asian countries. However, the currently planted varieties are all semi-domesticated landraces with delayed flowering and excessive height. These defects limit yield improvement per unit area and mechanized harvesting. In this study, a major QTL associated with flowering time and plant height in adlay has been mapped and identified as ClCCT, a gene having a conserved function and regulatory pathway for inhibiting flowering time and increasing plant height in gramineous crops. Among the six identified haplotypes of ClCCT, the haplotype with 38-bp insertion in promoter region of ClCCT has earlier flowering time and wider geographical distribution than other haplotypes. The insertion variation, which arises from the segmental duplication of ClCCT, can inhibit the expression level of reporter gene and has been used in breeding for early maturity and dwarfing. These research results not only reinforce our understanding of the importance of CCT domain protein in the tropical crops adapting to high-latitude environment, but also provide a validated breeding target for the early maturity and dwarfing of adlay.

Selecting an appropriate planting density is an effective way to improve crop water productivity (WP_C). However, there is a lack of research on the balance between evapotranspiration (ET) partitioning, water consumption, and grain production under different summer maize planting densities. To close this knowledge gap, a two-year field experiment was conducted in the North China Plain (NCP) to reveal the effects of different planting densities (HD: 100,000 plants ha⁻¹; MD: 78,000 plants ha⁻¹; LD: 56,000 plants ha⁻¹) on ET partitioning, grain yield, and water productivity of summer maize. The water-heat-carbon-nitrogen simulator (WHCNS) model was employed to calculate ET partitioning and perform scenario simulation after calibration and validation. The results showed that compared to the LD treatment, ET of the summer maize and grain yield in the MD and HD treatments significantly increased. Model simulations showed that the ratio of evaporation to ET ranged from 25.6% to 30.7% and reduced as increasing planting densities. Increasing planting density enhanced total transpiration of summer maize more than 20 mm, comparing to LD treatment, and the most significant differences between various planting densities appeared at the mid-growth stage (August 1 to 31). Scenario simulations indicated that grain yield and WP_C of summer maize were consistently higher in wet and normal years compared to drought years, exhibiting a trend of initially increasing and then decreasing with increasing planting density. The highest grain yield and WP_C of summer maize were observed at a planting density of approximately 80,000 plants ha⁻¹. The results provide theoretical support for selecting a summer maize planting density and effectively utilizing agricultural water in the NCP.

Near real-time maize phenology monitoring is crucial for field management, cropping system adjustments, and yield estimation. Most phenological monitoring methods are post-seasonal and heavily rely on high-frequency time-series data. These methods are not applicable on the unmanned aerial vehicle (UAV) platform due to the high cost of acquiring time-series UAV images and the shortage of UAV-based phenological monitoring methods. To address these challenges, we employed the Synthetic Minority Oversampling Technique (SMOTE) for sample augmentation, aiming to resolve the small sample modelling problem. Moreover, we utilized enhanced “separation” and “compactness” feature selection methods to identify input features from multiple data sources. In this process, we incorporated dynamic multi-source data fusion strategies, involving Vegetation index (VI), Color index (CI), and Texture features (TF). A two-stage neural network that combines Convolutional Neural Network (CNN) and Long Short-Term Memory Network (LSTM) is proposed to identify maize phenological stages (including sowing, seedling, jointing, trumpet, tasseling, maturity, and harvesting) on UAV platforms. The results indicate that the dataset generated by SMOTE closely resembles the measured dataset. Among dynamic data fusion strategies, the VI-TF combination proves to be most effective, with CI-TF and VI-CI combinations following behind. Notably, as more data sources are integrated, the model's demand for input features experiences a significant decline. In particular, the CNN-LSTM model, based on the fusion of three data sources, exhibited remarkable reliability when validating the three datasets. For Dataset 1 (Beijing Xiaotangshan, 2023: Data from 12 UAV Flight Missions), the model achieved an overall accuracy (OA) of 86.53%. Additionally, its precision (Pre), recall (Rec), F1 score (F1), false acceptance rate (FAR), and false rejection rate (FRR) were 0.89, 0.89, 0.87, 0.11, and 0.11, respectively. The model also showed strong generalizability in Dataset 2 (Beijing Xiaotangshan, 2023: Data from 6 UAV Flight Missions) and Dataset 3 (Beijing Xiaotangshan, 2022: Data from 4 UAV Flight Missions), with OAs of 89.4% and 85%, respectively. Meanwhile, the model has a low demand for input features, requiring only 54.55% (99 of all features). The findings of this study not only offer novel insights into near real-time crop phenology monitoring, but also provide technical support for agricultural field management and cropping system adaptation.

Timely identification and forecast of maize tasseling date (TD) are very important for agronomic management, yield prediction, and crop phenotype estimation. Remote sensing-based phenology monitoring has mostly relied on time series spectral index data of the complete growth season. A recent development in maize phenology detection research is to use canopy height (CH) data instead of spectral indices, but its robustness in multiple treatments and stages has not been confirmed. Meanwhile, because data of a complete growth season are needed, the need for timely in-season TD identification remains unmet. This study proposed an approach to timely identify and forecast the maize TD. We obtained RGB and light detection and ranging (LiDAR) data using the unmanned aerial vehicle platform over plots of different maize varieties under multiple treatments. After CH estimation, the feature points (inflection point) from the Logistic curve of the CH time series were extracted as TD. We examined the impact of various independent variables (day of year vs. accumulated growing degree days (AGDD)), sensors (RGB and LiDAR), time series denoise methods, different feature points, and temporal resolution on TD identification. Lastly, we used early CH time series data to predict height growth and further forecast TD. The results showed that using the 99th percentile of plot scale digital surface model and the minimum digital terrain model from LiDAR to estimate maize CH was the most stable across treatments and stages (R²: 0.928 to 0.943). For TD identification, the best performance was achieved by using LiDAR data with AGDD as the independent variable, combined with the knee point method, resulting in RMSE of 2.95 d. The high accuracy was maintained at temporal resolutions as coarse as 14 d. TD forecast got more accurate as the CH time series extended. The optimal timing for forecasting TD was when the CH exceeded half of its maximum. Using only LiDAR CH data below 1.6 m and empirical growth rate estimates, the forecasted TD showed an RMSE of 3.90 d. In conclusion, this study exploited the growth characteristics of maize height to provide a practical approach for the timely identification and forecast of maize TD.

The canonical CRISPR/Cas editors are constrained by the requirement for specific PAMs, which substantially limits their editable target range. Rice (particularly indica rice) is sensitive to low temperature, which impacts the yield and restricts the geographic distribution of rice. In this study, we developed PAM-flexible multiplex genome editing tools based on SpG (recognising NGN-PAMs) and SpRY (recognising NNN-PAMs) variants. We then tested the feasibility of using a sweet potato leaf curl virus (SPLCV) replicon-based expression vector and single-stranded DNA-binding domain (DBD) to improve the editing efficiency of these PAM-flexible editors. Furthermore, we used SpG-mediated multiplex genome editing to achieve comprehensive improvement in cold tolerance in indica rice by editing WRKY transcription factors OsWRKY53 and OsWRKY63, to generate high cold-resistant indica rice lines. We concluded that these PAM-flexible multiplex genome editors are powerful tools for multi-gene editing for crop genetic improvement.

Fusarium ear rot (FER) caused by Fusarium species severely reduces grain yield and quality of maize. Genome prediction (GP), a promising tool for quantitative trait breeding in plants and animals, uses molecular markers for capturing quantitative trait loci and predicting the genetic value of candidates for selection. In the present study, different subsets of markers and statistical methods for GP accuracy were tested in diverse inbred populations for FER resistance using a five-fold cross-validation approach. The prediction accuracy increased with an increase in the number of random markers; however, an increase in number beyond 10K did not increase the prediction accuracy. The prediction accuracy of selected markers was higher than that of random markers, and 500-1000 selected markers had the highest prediction accuracy, beyond which it slowly decreased. Although there was no difference among statistical methods when using selected markers at high prediction accuracy, significant differences were observed when using random markers. On this basis, a liquid chip named FER0.4K (liquid chip for genomic prediction of FER) containing 381 SNPs was developed for low-cost, high-throughput genotyping, with a prediction of approximately 0.82. The statistical method of genome prediction was compiled into a web-based, easy-to-use statistical analysis software using the “shiny” package in R. In summary, this study provides a foundation for FER resistance breeding in maize and offers new insights into the genetic improvement of other complex quantitative traits in plants.

Elevated atmospheric carbon dioxide concentration ([CO₂]) can stimulate crop growth and increase yield, but the effect may be constrained by soil contamination with heavy metals. In a free-air carbon dioxide enrichment experiment over three seasons, we found that soil heavy metal contamination can constrain or even reverse the projected CO₂ fertilization effect on rice yield. Elevated [CO₂] produced opposing effects on the accumulation of arsenic and cadmium in rice grain. Breeding crops for heavy-metal resistance and low arsenic accumulation may become necessary with continuing climate change.