Search Results (296)

Two-line hybrid rice breeding relies on photoperiod-/thermosensitive genic male sterile (P/TGMS) lines with reliable fertility transition across different environments. The fertility of japonica P/TGMS lines is intricately regulated by photoperiod and temperature, making it more challenging to breed japonica sterile lines with stable sterility than indica sterile lines. This complexity is one of the primary reasons the breeding and promotion of two-line japonica hybrid rice has lagged behind that of indica hybrid rice. Here, we report on Yun1032S, a novel japonica P/TGMS line bred in the low-latitude plateau. It was bred by crossing Peiai 64S, the famous P/TGMS line with the largest application area in China, with Yungengyou 1, a plateau japonica variety noted for its excellent cold tolerance and disease resistance. Yun1032S exhibited stable sterility and female-parent traits favorable for two-line seed production. The elite combination YLY7706 (Yunliangyou7706), derived from a cross between Yun1032S and Yungenghui7501, showed a stable and competitive yield and strong disease resistance in the 2022–2023 Yunnan provincial regional trials. To analyze the genetic basis of phenotypes, we performed whole-genome resequencing and functional loci analysis of the parents and found that they carry a great number of superior alleles, which account for their yield and disease-resistant performance. To assess the breeding value of Yun1032S, we analyzed heterosis of a new batch of combinations derived from Yun1032S and identified a new combination, Jian3, with greater yield potential than YLY7706. These findings not only enhance the breeding of japonica P/TGMS lines but also provide direction for future pairing of two-line hybrid combination breeding. The study presents innovative concepts that further integrate genomics with traditional breeding techniques. Ultimately, Yun1032S marks a significant milestone in japonica P/TGMS line breeding technology, opening new avenues for the development of the two-line system. Full article

Ascochyta blight remains a major constraint for field pea (Pisum sativum L.) production and a priority for breeding programmes. So far, only moderate levels of incomplete resistance have been identified in pea germplasm and accumulated in pea cultivars by breeding. Resistance identified so far appears to be of complex inheritance, with phenotypic expression strongly affected by plant phenology and morphology and by environ-mental factors. This has slowed down the development and release of resistant elite cultivars. In this work, we describe the development of novel resistant breeding lines derived from targeted intra- and interspecific crosses combined with cycles of selection under high disease pressure at seedling and adult plant stages. The performance of thirteen breeding lines selected for improved resistance and good agronomic traits was further validated in a comparative field trial. Results confirmed the successful combination of competitive yield and good standing ability with good levels of resistance exceeding those of the resistant check. These advanced breeding lines are available on request for research and breeding use. Full article

Mulberry (Morus alba L.) is a woody plant primarily cultivated for silkworm breeding, with significant economic and ecological functions. Its nitrogen use efficiency directly affects leaf yield, quality, and environmental adaptability. The main inorganic nitrogen forms available for plant uptake in soil are ammonium nitrogen and nitrate nitrogen, and plant uptake and assimilation of these two nitrogen sources often exhibit species-specific preferences. This review systematically summarizes the research progress on nitrogen uptake preferences in mulberry, confirming that this species generally shows a preferential uptake of nitrate. Specifically, when supplied with nitrate or a mixed nitrogen source dominated by nitrate, mulberry exhibits better performance in growth and development, photosynthetic efficiency, and accumulation of secondary metabolites. This review further discusses the physiological characteristics and underlying regulatory mechanisms responsible for this preference, and analyzes key factors affecting nitrogen uptake preferences, including soil properties, environmental stresses, and microbial interactions. It should be noted that while controlled experiments have yielded important insights, the applicability of these findings under complex field conditions still requires further validation through field trials. Finally, future research directions are prospected, including in-depth dissection of molecular mechanisms, field validation, plant-microbe interactions, and nutritional strategies for stress resistance, aiming to provide a theoretical basis for efficient cultivation and precise nitrogen management of mulberry. Full article

Drought stress is a significant environmental factor affecting plant growth, fruit quality and distribution. Wild jujube is an important species of eco-economic forest tree. In this study, two wild jujube families, ‘NO. 1’ (tolerant) and ‘NO. 5’ (sensitive), which show significant differences in morphological and physiological indicators in drought treatment, are considered. Compared with the ‘NO. 5’, the ‘NO. 1’ exhibited lower water loss, leaf yellowing and abscission rates, as well as reduced malondialdehyde (MDA) content, while showing higher superoxide dismutase (SOD) activity and elevated levels of soluble sugars (SS), soluble proteins (SP), and proline (Pro). In contrast, the ‘NO. 5’ suffered more severe damage to leaf epidermal cells compared with the ‘NO. 1’, accompanied by a significant decline in net photosynthetic rate (A) and instantaneous water use efficiency (WUEi). Transcriptomic profiles between two wild jujube families with markedly different drought responses (withholding water for 15 days) are shown. The two wild jujube families included 3238 up-regulated and 2675 down-regulated differentially expressed genes (DEGs). Many DEGs enriched in the GO and KEGG pathways are related to antioxidant activity, transmembrane transport, carbohydrate biosynthesis and metabolism, plant hormones, and photosynthesis. The biosynthesis of amino acids, the MAPK signaling pathway, plant hormone signal transduction, and flavonoid and alkaloid biosynthesis were the transcriptome modifications most significantly altered by drought stress. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to verify the precision of the RNA-seq data. ZjJIP23-1, ZjbZIP53, ZjSPS8, ZjCAO, ZjADH1 and ZjERF39 may play important roles in the drought tolerance of the wild jujube. This study provides a solid foundation for further studies on the complex mechanisms and breeding of drought-resistant plants in wild jujube. Full article

Rapeseed (Brassica napus L.) faces escalating threats from abiotic and biotic stresses, notably blackleg caused by Leptosphaeria maculans. Due to limited chemical control efficacy and stringent GMO regulations, marker-assisted selection (MAS) leveraging natural genetic variation has become an indispensable strategy for crop improvement. This study identified novel molecular markers for blackleg resistance by integrating genome-wide association study (GWAS) results with high-throughput genotyping by Diversity Arrays Technology sequencing. Phenotypic screening across the population demonstrated a wide spectrum of disease severity (scores 0–6), confirming the segregation of key resistance genes. The DArTseq platform identified nearly 104,000 markers, comprising 61% SilicoDArTs and 39% SNPs. Among the 33 most significant markers associated with resistance (p < 0.01), 76% were SilicoDArTs. Transcriptomic data further validated these findings, revealing 13 marker-linked genes expressed during infection, seven of which exhibited significant differential expression. Comprehensive functional annotation of Arabidopsis thaliana orthologs associated these genes with diverse cellular and plant-wide processes, particularly during stress responses. Collectively, these findings emphasize the complex polygenic nature of blackleg resistance and provide robust genomic tools for the accelerated breeding of resilient B. napus cultivars. Full article

Background: The global transcriptome reprogramming in grapevines in response to powdery mildew remains poorly understood, despite its economic implications, especially the new cultivars. Methods: Thus, this study aimed to elucidate these changes through RNA sequencing in ‘Yeniang No. 2’ grapevine leaves infected with powdery mildew compared to healthy ones. Results: A total of six samples were subjected to transcriptome sequencing, resulting in 36.85 Gb of clean data. A minimum of 5.89 Gb of clean data was generated for each sample, with at least 92.24% of the clean data attaining a quality score of Q30. Clean reads from each sample were aligned to the designated reference genome. The mapping ratio varied between 88.77% and 89.66%. The high-quality sequencing data revealed 1219 differentially expressed genes (DEGs), of which the infection upregulated 790 and downregulated 429. Functional enrichment analyses revealed a significant activation of key defense-related pathways. These included plant–pathogen interaction, phenylpropanoid and flavonoid biosynthesis for creating antimicrobial compounds, glutathione metabolism for reducing oxidative stress, and oxidative phosphorylation for enhanced energy production. This indicates a coordinated, multi-faceted defense strategy. The study also uncovered a complex layer of post-transcriptional regulation, identifying 1883 novel genes and 22,210 alternative splicing events, primarily skipped exons and intron retention. Key hub proteins identified within interaction networks, along with these splicing changes, underscore a sophisticated defense involving transcriptional reprogramming and metabolic shifts. Conclusions: The genes and molecular markers discovered are valuable resources for marker-assisted breeding. Leveraging these findings, particularly hub genes and favorable splice variants, can accelerate the development of new grapevine cultivars with durable resistance to powdery mildew. Full article

Metabolomics, representing the biochemical phenotype of cells or tissues, serves as an intrinsic factor underlying the differences in plant traits. Recent advances in multi-omics technologies have significantly deepened our understanding of plant metabolic diversity, enabling researchers to dissect complex biochemical networks at unprecedented levels of detail. This review explores the integration of metabolomics with genomics, transcriptomics, proteomics, epigenomics, microbiomics, and other omics approaches, emphasizing the power of these combined approaches in unraveling the molecular mechanisms underlying plant adaptation, stress resistance, and phenotypic variation. Through a critical analysis of representative case studies across diverse crops, we demonstrate how multi-omics strategies facilitate the identification of key metabolic pathways and regulatory networks for crop improvement. We also discuss current challenges in data integration, metabolite coverage, and the functional characterization of unknown compounds, and propose future directions for overcoming these limitations. Addressing these challenges will require both the enhanced resolution and sensitivity of analytical techniques, as well as more robust frameworks for data integration and interpretation. By overcoming these challenges, the convergence of metabolomics with other omics disciplines will continue to expand our understanding of plant biology, offering novel insights and innovation in crop breeding and sustainable agriculture. Full article

Low temperature and drought are among the most pervasive abiotic stresses limiting crop productivity worldwide, and their frequent co-occurrence or alternation imposes compounded constraints on agricultural sustainability. Increasing evidence supports cross-tolerance, whereby exposure to one stress enhances resistance to another, as an emergent property of shared signaling networks and integrative regulatory layers. In this review, we summarize recent advances in understanding cold–drought cross-talk, from early stress perception and secondary messengers to hormonal coordination via abscisic acid, transcriptional reprogramming centered on dehydration responsive element binding protein/C repeat binding factor (DREB/CBF) modules, and longer-term regulatory memory mediated by chromatin remodeling and biomolecular condensates. Importantly, we further discuss how these mechanistic insights can be translated into precision breeding strategies, including genome editing, allele mining, and backcross-assisted introgression, to accelerate the development of crop varieties with stable multi-stress tolerance. Finally, we highlight future directions for integrating multi-omics, high-throughput phenotyping, and data-driven approaches to enable efficient molecular design breeding for complex stress environments. Full article

Aspergillus flavus infection and accumulation of carcinogenic aflatoxins are detrimental to maize (Zea mays) production and consumption. We investigated lncRNA–RBP interactions during maize–A. flavus crosstalk using transcriptomic profiling, structural analysis, molecular docking simulations, and machine learning approaches. Analysis of 18 RNA-seq datasets identified 2104 lncRNAs in maize, of which 461 were differentially expressed under A. flavus infection. Distinct lncRNAs were preferentially induced under infection (e.g., Zm00001eb303170) or normal germination (e.g., Zm00001eb144150, Zm00001eb406410). RNA secondary structure predictions indicated high structural heterogeneity and thermodynamic stability, consistent with dynamic regulatory potential. Docking simulations with six key RNA binding proteins (RBPs)—including branch point bridging protein (BPB), KH domain protein, and pentatricopeptide repeat (PPR) proteins—demonstrated strong lncRNA–protein binding, with the lncRNA1–BPB complex exhibiting the highest binding affinity. ML algorithms identified the crucial role of tryptophan in determining interactions, while lncRNA17-KH and lncRNA1-BP complexes were found to have the best interaction under normal germination and A. flavus infection, respectively. The lncRNA–miRNA–mRNA regulatory network highlighted lncRNAs functioning as decoys or precursors of stress-responsive miRNAs (e.g., zma-miR156, zma-miR164, zma-miR399). These interactions targeted transcriptional regulators, splicing factors, and metabolic enzymes implicated in stress tolerance, seed germination, and systemic acquired resistance. The maize lncRNAs are active regulatory molecules embedded in complex RBP and miRNA interaction networks that fine-tune gene expression during A. flavus infection. The study provides novel insights into lncRNA-mediated resistance mechanisms and offers potential molecular targets for breeding or gene editing to mitigate aflatoxin contamination. Full article

The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family, a group of plant-specific transcription factors, plays a key role in plant growth and development through complex regulatory networks. Within this family, SPL9 has been identified as a key regulator of diverse biological processes. In this review, we summarize the current knowledge on SPL9, focusing on its expression regulatory mechanisms and roles in plant development, such as morphogenesis, reproductive processes, and crop yield determinations. We further describe its role in plant responses to abiotic and biotic stresses and its integration into broader regulatory networks. We also outline future research priorities and discuss potential applications of SPL9-based strategies in molecular design breeding to increase crop productivity and stress resistance. Full article

Genomic selection (GS) is a promising tool to accelerate genetic gain for complex traits. In this study, we evaluated the potential of GS for the improvement of seven lodging-related traits in double-cropping rice in Southern China using 438 rice accessions. The traits examined included the length and bending resistance of the third and fourth internodes (IL3, IL4, BR3, BR4), plant height (PH), and the ratio of internode length to plant height (IL3/PH, IL4/PH). Significant phenotypic differences were observed for all traits between the two seasons. In comparisons of cross-validation and independent prediction, GBLUP and BayesLASSO outperformed LightGBM across all traits in both seasons. Across all evaluated traits, prediction accuracies (Pearson’s r) ranged from 0.33 to 0.78 in cross-validation and from 0.28 to 0.75 in independent prediction using the GBLUP model. Bending resistance exhibited lower prediction accuracy due to its lower genomic heritability. Correlation analysis revealed that plant height was not significantly correlated with culm bending resistance, suggesting that these traits are genetically independent. We utilized GBLUP models trained on our experimental data to predict the genomic estimated breeding values (GEBVs) of the 3000 Rice Genomes Project (3kRG) dataset. The results demonstrated that GS can efficiently enrich the proportion of highly lodging-resistant accessions, increasing it from 31.40% in the base 3kRG population to a maximum of 83.00% among the top 200 selected individuals. Furthermore, indirect selection for traits with higher heritability, such as IL and IL/PH, was more effective at screening highly lodging-resistant cultivars than direct selection for BR. Our research demonstrates the feasibility of applying genomic selection for the breeding of lodging-resistant varieties in double-cropping rice and provides a foundation for further applications. Full article

Domestic cattle represent one of the most significant evolutionary successes in the history of human–animal mutualism. This review synthesizes evidence from paleogenomics and modern population genetics, particularly recent pangenome analyses, to reconstruct a comprehensive evolutionary trajectory of cattle. We outline the two domestication events: the emergence of taurine cattle (Bos taurus) in the Fertile Crescent (~10,500 years ago) and zebu cattle (Bos indicus) in the Indus Valley (~8000 years ago). Following domestication, cattle dispersed globally alongside human migration, resulting in a complex genetic mosaic shaped by introgression with wild relatives and extensive admixture between lineages. By integrating data from mitochondrial DNA, Y-chromosome haplotypes, and whole-genome sequencing of modern, ancient, and wild samples, we reconstruct the detailed global dispersal of cattle. Furthermore, we dissect the molecular mechanisms underlying phenotypic diversity, emphasizing how natural selection has driven environmental adaptation, how artificial selection has optimized production traits, and how the emerging bovine pangenome is unveiling “hidden” genetic variations critical for climate resilience and disease resistance. Ultimately, this review summarizes the origin, dispersal, and genomic diversity of cattle, offering vital insights for the conservation of indigenous genetic resources and the advancement of molecular breeding strategies in the face of a changing global climate. Full article

Plant RNA interference (RNAi) is a fundamental antiviral defense that relies on coordinated activities of DICER-like endonucleases (DCLs), Argonaute proteins (AGOs) and RNA-dependent RNA polymerases (RDRs). Over the past decades, studies using model and crop species have uncovered complex and often redundant roles for DCLs and RDRs in generating and amplifying virus-derived small interfering RNAs (vsiRNAs), in addition to connections with transcriptional gene silencing (TGS) and epigenetic defenses against DNA viruses. Concurrently, plant viruses have evolved diverse counterstrategies—proteinaceous RNA silencing suppressors (RSSs), exoribonuclease (XRN)-resistant noncoding RNAs, and indirect manipulation of host pathways—to evade RNAi. Driven by the co-evolutionary arms race, plants have developed sophisticated counter-countermeasures that modulate or overcome viral anti-RNAi activity. Accumulated evidence suggests that plants encode host factor genes that are activated to degrade or sequester viral components such as RSSs against viral infection. On the other hand, plants have also evolved endogenous host modulators of antiviral RNAi that can either reinforce the antiviral response or be co-opted by viruses to antagonize it, representing a furious dynamic molecular battling mechanism. Here, we review recent advances in the molecular functions of DCLs and RDRs across species, summarize newly discovered viral counter-defenses (including RNA-based suppressors), and discuss host counter-countermeasures. We research key areas—such as the roles of RDRγ-class proteins, RTL1 (RNase three-like 1)-mediated competition with DCLs, and the mechanistic impact of viral noncoding RNAs—and outline translational opportunities for improving virus resistance in crops through breeding, biotechnological approaches, and RNA-based applications. Full article

The colored-leaf Osmanthus fragrans is a valuable ornamental tree species that integrates greenery, colorful leaves, and fragrance. At present, research on colored-leaf Osmanthus fragrans mainly focuses on cultivar breeding, classification and cultivation, and physiological resistance, while studies on leaf color variation remain limited. In this study, the colored-leaf Osmanthus cultivar ‘Jinyu Guihua’ and its female parent were used as materials. The leaf coloration mechanism was systematically investigated through a combined analysis of physiology, transcriptomics, and metabolomics. The results showed that compared with the female parent, the leaves of ‘Jinyu Guihua’ exhibited significantly reduced chlorophyll b and anthocyanin contents, fewer chloroplasts, and more plastoglobules. Transcriptomic analysis identified 3938 differentially expressed genes (DEGs), among which the key chlorophyll metabolism gene CAO was downregulated and NOL was upregulated; the key carotenoid synthesis gene PSY was downregulated and CYP97A3 was upregulated; the key anthocyanin synthesis gene ANS was downregulated; and the PetC2 gene in the photosynthesis-related Cytb6-f complex was upregulated. qRT-PCR validation results were consistent with the RNA-seq data. Metabolomic analysis detected 1290 metabolites, classified into 21 subcategories, with flavonoids being the most abundant (17.21%). Anthocyanin synthase (ANS) significantly downregulated the expression levels of cyanidin-3-O-rutinoside (Cy3R) and delphinidin-3-O-rutinoside (De3R). In conclusion, the leaf color variation in ‘Jinyu Guihua’ is closely related to changes in leaf pigment content and the regulation of key metabolic pathway gene expression. The findings of this study provide a theoretical basis for the molecular breeding of new colored-leaf Osmanthus varieties and serve as a reference for trait research in other ornamental plants. Full article

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism in eukaryotes. Plants can cope with complex environmental changes through AS. In this paper, we found that AS plays an important role in plant responses to biotic and abiotic stresses. First, we note that under biotic stress (e.g., disease, insects), AS regulates the expression of immune-related genes and produces splice variants with different functions to regulate plant disease resistance. Second, under abiotic stress (e.g., drought, cold, heat, salt), plants generate functional splice variants via different AS events and change the original function of the gene. At the same time, we also found that splicing factors and regulatory elements, such as serine/arginine-rich proteins associated with AS, are also involved in the regulation of the expression of related resistance genes to improve plant stress resistance. Therefore, this review summarizes the recent progress on the main types of AS events, the functions of related splicing factors, and the action routes and regulatory mechanisms of splice variants. We hope to provide a reference for further understanding of the stress response mechanism of plant AS and provide a theoretical basis for the breeding of resistant varieties. Full article